[
    {
        "name": "SC_ATAC_GEX_COUNTER_CS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                },
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "skip_compatibility_check",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "rna_include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "k_means_max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "no_bam",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "analysis",
                            "type": "AnalysisOutput",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "clustering": {
                                    "atac": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    },
                                    "gex": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    }
                                },
                                "dimensionality_reduction": {
                                    "atac": {
                                        "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                                        "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                                        "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                                        "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                                        "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_umap_csv/2_components/projection.csv"
                                    },
                                    "gex": {
                                        "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                                        "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                                        "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                                        "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                                        "pca_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_umap_csv/2_components/projection.csv"
                                    }
                                },
                                "feature_linkage": {
                                    "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                    "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                                },
                                "tf_analysis": {
                                    "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                                    "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                                    "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "web_summary",
                            "type": "html",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-ud0d5b6cdcd/files/web_summary.html",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary_csv_cs.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics_cs.csv",
                            "waiting": false
                        },
                        {
                            "id": "filtered_feature_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_filtered_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "filtered_feature_bc_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_feature_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "raw_feature_bc_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "cloupe",
                            "type": "cloupe",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-ud0d5b6cdcd/files/output_for_cloupe.cloupe",
                            "waiting": false
                        },
                        {
                            "id": "gex_possorted_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam",
                            "waiting": false
                        },
                        {
                            "id": "gex_possorted_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam.bai",
                            "waiting": false
                        },
                        {
                            "id": "gex_molecule_info",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/molecule_info_non_multiplexed.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_possorted_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam",
                            "waiting": false
                        },
                        {
                            "id": "atac_possorted_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam.bai",
                            "waiting": false
                        },
                        {
                            "id": "atac_fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "atac_fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "atac_peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "atac_cut_sites",
                            "type": "bigwig",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-ud0d5b6c57b/files/cut_sites.bigwig",
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_annotation",
                            "type": "tsv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ARC_COUNTER_PREFLIGHT_LOCAL",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.ARC_COUNTER_PREFLIGHT_LOCAL",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "on_cluster",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                },
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "k_means_max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r1_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r2_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": null
                }
            }
        ],
        "edges": [],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/preflight/arc_counter_preflight"
    },
    {
        "name": "SC_ATAC_GEX_COUNTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                },
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "skip_compatibility_check",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "k_means_max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "no_bam",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "rna_chemistry",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "ARC-v1",
                            "waiting": false
                        },
                        {
                            "id": "rna_custom_chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_recovered_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1000,
                            "waiting": false
                        },
                        {
                            "id": "rna_subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "rna_initial_reads",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r1_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r2_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_feature_reference",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "rna_trim_polya_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "rna_trim_tso_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "atac_subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "atac_custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "disable_bc_multiplets",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "web_summary",
                            "type": "AnalysisHTML",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": null,
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-ud0d5b6cdcd/files/web_summary.html",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/web_summary.html"
                            },
                            "waiting": false
                        },
                        {
                            "id": "summary_csv",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary_csv_cs.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics_cs",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics_cs.csv",
                            "waiting": false
                        },
                        {
                            "id": "filtered_feature_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_filtered_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "filtered_feature_bc_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_feature_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "raw_feature_bc_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "analysis",
                            "type": "AnalysisOutput",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "clustering": {
                                    "atac": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    },
                                    "gex": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    }
                                },
                                "dimensionality_reduction": {
                                    "atac": {
                                        "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                                        "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                                        "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                                        "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                                        "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_umap_csv/2_components/projection.csv"
                                    },
                                    "gex": {
                                        "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                                        "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                                        "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                                        "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                                        "pca_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_umap_csv/2_components/projection.csv"
                                    }
                                },
                                "feature_linkage": {
                                    "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                    "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                                },
                                "tf_analysis": {
                                    "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                                    "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                                    "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "cloupe",
                            "type": "cloupe",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-ud0d5b6cdcd/files/output_for_cloupe.cloupe",
                            "waiting": false
                        },
                        {
                            "id": "gex_possorted_genome_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam",
                            "waiting": false
                        },
                        {
                            "id": "gex_possorted_genome_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam.bai",
                            "waiting": false
                        },
                        {
                            "id": "gex_molecule_info",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/molecule_info_non_multiplexed.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_possorted_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam",
                            "waiting": false
                        },
                        {
                            "id": "atac_possorted_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam.bai",
                            "waiting": false
                        },
                        {
                            "id": "atac_fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "atac_fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "atac_peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "atac_cut_sites",
                            "type": "bigwig",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-ud0d5b6c57b/files/cut_sites.bigwig",
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_annotation",
                            "type": "tsv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "is_multi_genome",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "pd_gex_inputs",
                            "type": "PdGEXInputs",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "alignments": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/pos_sorted.asf",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/pos_sorted.asf"
                                ],
                                "annotation_files": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4"
                                ],
                                "barcode_summary_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                                "barcode_whitelist": "737K-arc-v1",
                                "filtered_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                                "filtered_gene_bc_matrices_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "gem_groups": [
                                    1
                                ],
                                "is_multi_genome": false,
                                "per_barcode_metrics": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-ud0d5b6cc91/files/augmented_metrics.csv",
                                "raw_gene_bc_matrices_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                                "read_shards": {
                                    "corrected_reads": [
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                                    ],
                                    "invalid_reads": [
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                                    ],
                                    "valid_reads": [
                                        "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                                    ]
                                },
                                "summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/metrics_summary_json.json"
                            },
                            "waiting": false
                        },
                        {
                            "id": "pd_atac_inputs",
                            "type": "PdATACInputs",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "basic_summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                                "bulk_complexity": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/bulk_complexity.json",
                                "cell_calling_summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-ud0d5b6cc91/files/merged_summary.json",
                                "complexity_summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/complexity_summary.json",
                                "count_dict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                                "ctcf_relpos": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                                "enrichment_results": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-ud0d5b6c6e2/files/summary_metrics.json",
                                "excluded_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                                "filtered_peak_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "insert_summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-ud0d5b6c567/files/insert_summary.json",
                                "peak_summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                                "sample_def": [
                                    {
                                        "fastq_id": null,
                                        "fastq_mode": "ILMN_BCL2FASTQ",
                                        "gem_group": null,
                                        "lanes": null,
                                        "library_type": "Chromatin Accessibility",
                                        "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                        "sample_indices": [
                                            "any"
                                        ],
                                        "sample_names": [
                                            "samp26"
                                        ],
                                        "subsample_rate": null,
                                        "target_set": null,
                                        "target_set_name": null
                                    }
                                ],
                                "sc_insert_sizes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                                "singlecell": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                                "singlecell_complexity": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/singlecell_complexity.json",
                                "singlecell_results": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6ccec/files/summary.json",
                                "tss_relpos": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv"
                            },
                            "waiting": false
                        },
                        {
                            "id": "analysis_h5",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/analysis_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "analysis_summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ARC_COUNTER_PREFLIGHT",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ARC_COUNTER_PREFLIGHT",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "on_cluster",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                },
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "k_means_max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r1_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_r2_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": null
                }
            }
        ],
        "edges": [],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/preflight/arc_counter_preflight"
    },
    {
        "name": "ATAC_GEX_CLOUPE_PREPROCESS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 7.294921875,
                    "__vmem_gb": 10.294921875
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "pipestance_type",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "SC_ATAC_GEX_COUNTER",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "analysis",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/analysis_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "feature_barcode_matrix",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/loupe_matrix_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "metrics_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "aggregation_csv",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "gem_group_index_json",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "no_secondary_analysis",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "output_for_cloupe",
                            "type": "cloupe",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-ud0d5b6cdcd/files/output_for_cloupe.cloupe",
                            "waiting": false
                        },
                        {
                            "id": "gem_group_index_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/cloupe/atac_cloupe_preprocess"
    },
    {
        "name": "CHECK_JOINT_BARCODES_COMPATIBILITY",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "atac_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.json",
                            "waiting": false
                        },
                        {
                            "id": "gex_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/bc_counts_json.json",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        }
                    ],
                    "Return": null
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/check_joint_barcodes_compatibility"
    },
    {
        "name": "COMPILE_GEX_BARCODE_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/per_barcode_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "augmented_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-ud0d5b6cc91/files/augmented_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "wasted_data_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-ud0d5b6cc91/files/wasted_data_metrics.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/reporter/compile_gex_barcode_metrics"
    },
    {
        "name": "CREATE_JOINT_WEBSUMMARY",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 16,
                    "__vmem_gb": 19
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 1,
                            "__vmem_gb": 19
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "merge_singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "analysis_csv",
                            "type": "AnalysisOutput",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "clustering": {
                                    "atac": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    },
                                    "gex": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    }
                                },
                                "dimensionality_reduction": {
                                    "atac": {
                                        "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                                        "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                                        "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                                        "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                                        "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_umap_csv/2_components/projection.csv"
                                    },
                                    "gex": {
                                        "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                                        "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                                        "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                                        "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                                        "pca_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_umap_csv/2_components/projection.csv"
                                    }
                                },
                                "feature_linkage": {
                                    "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                    "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                                },
                                "tf_analysis": {
                                    "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                                    "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                                    "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "atac_data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-ud0d5b6cd0c/files/data.json",
                            "waiting": false
                        },
                        {
                            "id": "gex_data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/ws_data.json",
                            "waiting": false
                        },
                        {
                            "id": "debug",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "rna_include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "web_summary",
                            "type": "html",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-ud0d5b6cdcd/files/web_summary.html",
                            "waiting": false
                        },
                        {
                            "id": "data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-ud0d5b6cdcd/files/data.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/reporter/create_joint_websummary"
    },
    {
        "name": "GEX_SUMMARIZE_REPORTS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 8,
                    "__vmem_gb": 11
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "summaries",
                            "type": "json[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-ud0d5b6cd6e/files/summary.json"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "analysis",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "barcode_summary_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_gene_bc_matrices_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "gem_groups",
                            "type": "int[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                1
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "per_feature_metrics_csv",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "metrics_summary_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/metrics_summary_json.json",
                            "waiting": false
                        },
                        {
                            "id": "metrics_summary_csv",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/metrics_summary_csv.csv",
                            "waiting": false
                        },
                        {
                            "id": "web_summary",
                            "type": "html",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/web_summary.html",
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/feature_reference.csv",
                            "waiting": false
                        },
                        {
                            "id": "ws_data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/ws_data.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/summarize_reports"
    },
    {
        "name": "MERGE_RNA_ATAC_DATA",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "disable_atac",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "disable_rna",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "atac_summary_csv_cs",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary_csv.csv",
                            "waiting": false
                        },
                        {
                            "id": "rna_summary_csv_cs",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/metrics_summary_csv.csv",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "atac_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "rna_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "atac_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "rna_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-ud0d5b6cc91/files/augmented_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "joint_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "atac_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "rna_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_atac_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_rna_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "rna_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-ud0d5b6cd77/files/metrics_summary_json.json",
                            "waiting": false
                        },
                        {
                            "id": "atac_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "joint_summaries",
                            "type": "json[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-ud0d5b6cc91/files/merged_summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/summary.json"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "metrics_cs",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics_cs.csv",
                            "waiting": false
                        },
                        {
                            "id": "metrics_cells_only",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/metrics_cells_only.csv",
                            "waiting": false
                        },
                        {
                            "id": "matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "summary_csv_cs",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-ud0d5b6cd7d/files/summary_csv_cs.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/merge_rna_atac_data"
    },
    {
        "name": "SPLIT_SAMPLE_DEF",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                },
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "atac_sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "rna_sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/split_sample_def"
    },
    {
        "name": "WRITE_POS_BAM",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    0,
                                    202962286,
                                    6961322419353871089,
                                    3499212506,
                                    1040
                                ],
                                "start": null
                            },
                            "write_header": true
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    2,
                                    840310,
                                    1701054579734691293,
                                    2411687570,
                                    1040
                                ],
                                "start": [
                                    0,
                                    202962286,
                                    6961322419353871089,
                                    3499212506,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    3,
                                    25219826,
                                    9358522110411218963,
                                    2614034295,
                                    1040
                                ],
                                "start": [
                                    2,
                                    840310,
                                    1701054579734691293,
                                    2411687570,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    5,
                                    92145725,
                                    16154183184937840378,
                                    2411687570,
                                    1024
                                ],
                                "start": [
                                    3,
                                    25219826,
                                    9358522110411218963,
                                    2614034295,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    8,
                                    31236759,
                                    16476189754548073689,
                                    2411687570,
                                    16
                                ],
                                "start": [
                                    5,
                                    92145725,
                                    16154183184937840378,
                                    2411687570,
                                    1024
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    10,
                                    42906947,
                                    10966414876112993667,
                                    1527582566,
                                    1040
                                ],
                                "start": [
                                    8,
                                    31236759,
                                    16476189754548073689,
                                    2411687570,
                                    16
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    11,
                                    171713849,
                                    17610602571382521876,
                                    2411687570,
                                    1024
                                ],
                                "start": [
                                    10,
                                    42906947,
                                    10966414876112993667,
                                    1527582566,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    13,
                                    41183145,
                                    7171368277878180676,
                                    1594160002,
                                    1040
                                ],
                                "start": [
                                    11,
                                    171713849,
                                    17610602571382521876,
                                    2411687570,
                                    1024
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    16,
                                    2005382,
                                    2341217194497485912,
                                    2411687570,
                                    0
                                ],
                                "start": [
                                    13,
                                    41183145,
                                    7171368277878180676,
                                    1594160002,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    17,
                                    78195282,
                                    18091755832241613610,
                                    2487197176,
                                    0
                                ],
                                "start": [
                                    16,
                                    2005382,
                                    2341217194497485912,
                                    2411687570,
                                    0
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    18,
                                    87085799,
                                    10360315123321028987,
                                    134138731,
                                    1040
                                ],
                                "start": [
                                    17,
                                    78195282,
                                    18091755832241613610,
                                    2487197176,
                                    0
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    19,
                                    93890633,
                                    15791840933492026571,
                                    4201856914,
                                    1040
                                ],
                                "start": [
                                    18,
                                    87085799,
                                    10360315123321028987,
                                    134138731,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    21,
                                    95045810,
                                    14138045143300795057,
                                    2487197176,
                                    1024
                                ],
                                "start": [
                                    19,
                                    93890633,
                                    15791840933492026571,
                                    4201856914,
                                    1040
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": [
                                    51,
                                    117719,
                                    4717939049086723716,
                                    916497403,
                                    0
                                ],
                                "start": [
                                    21,
                                    95045810,
                                    14138045143300795057,
                                    2487197176,
                                    1024
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 2,
                            "__vmem_gb": 5,
                            "range": {
                                "end": null,
                                "start": [
                                    51,
                                    117719,
                                    4717939049086723716,
                                    916497403,
                                    0
                                ]
                            },
                            "write_header": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "sample_barcodes_json",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "no_bam",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "bam_header",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud0d5b6b8be/files/bam_header",
                            "waiting": false
                        },
                        {
                            "id": "alignments",
                            "type": "asf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/pos_sorted.asf"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "pos_sorted_bam",
                            "type": "SampleBamFile",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": {
                                "bam_file": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam",
                                "bam_index_file": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-ud0d5b6cc83/files/pos_sorted_non_multiplexed.bam.bai",
                                "sample": "non_multiplexed"
                            },
                            "waiting": false
                        },
                        {
                            "id": "multi_pos_sorted_bam",
                            "type": "SampleBamFile[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_pos_bam"
    },
    {
        "name": "_ATAC_MATRIX_COMPUTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "chunks",
                            "type": "FastqDef[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist_path",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
                            "waiting": false
                        },
                        {
                            "id": "custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "no_bam",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "assay",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "arc",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "possorted_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam",
                            "waiting": false
                        },
                        {
                            "id": "possorted_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam.bai",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "cut_sites",
                            "type": "bigwig",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-ud0d5b6c57b/files/cut_sites.bigwig",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_mapping",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "peak_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                            "waiting": false
                        },
                        {
                            "id": "raw_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_peak_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        },
                        {
                            "id": "basic_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "bc_counts_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.json",
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/frag_bc_counts.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ALIGN_ATAC_READS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 9981184,
                                "start": null
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 19962368,
                                "start": 9981184
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 29943552,
                                "start": 19962368
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 39924736,
                                "start": 29943552
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 49905920,
                                "start": 39924736
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 59878912,
                                "start": 49905920
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 69860096,
                                "start": 59878912
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 79841280,
                                "start": 69860096
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 89822464,
                                "start": 79841280
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 99803648,
                                "start": 89822464
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 109784832,
                                "start": 99803648
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 119766016,
                                "start": 109784832
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 129747200,
                                "start": 119766016
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 139728384,
                                "start": 129747200
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 149709568,
                                "start": 139728384
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 159682560,
                                "start": 149709568
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 169663744,
                                "start": 159682560
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 179644928,
                                "start": 169663744
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 189626112,
                                "start": 179644928
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 199607296,
                                "start": 189626112
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 209588480,
                                "start": 199607296
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 219569408,
                                "start": 209588480
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 229550592,
                                "start": 219569408
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 239531776,
                                "start": 229550592
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 249512960,
                                "start": 239531776
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 259485952,
                                "start": 249512960
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 269467136,
                                "start": 259485952
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 279448320,
                                "start": 269467136
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": 289429504,
                                "start": 279448320
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 12,
                            "__threads": 4,
                            "__vmem_gb": 15,
                            "range": {
                                "end": null,
                                "start": 289429504
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "heartbeat",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-ud0d5b69fed/files/out.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "chunk_chemistry_map",
                            "type": "string[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": [
                                "3p;rev"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "bch.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.bch.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist_path",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
                            "waiting": false
                        },
                        {
                            "id": "chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "num_read_pairs",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": 299406391,
                            "waiting": false
                        },
                        {
                            "id": "assay",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "arc",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "aligned_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud0d5b6a421/files/aligned_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "unaligned_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud0d5b6a421/files/unaligned_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "stats",
                            "type": "map",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                            "matchedFork": null,
                            "value": {
                                "footprint": {
                                    "denominator": 299406391,
                                    "numerator": 299106562
                                },
                                "high_mapq": {
                                    "denominator": 598812782,
                                    "numerator": 530237987
                                },
                                "num_read_pairs": 299406391,
                                "valid_barcode": {
                                    "denominator": 299406391,
                                    "numerator": 295701081
                                }
                            },
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian align_atac_reads"
    },
    {
        "name": "GENERATE_PEAK_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 2.6728515625,
                    "__vmem_gb": 5.6728515625
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_0.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_1.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_2.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_3.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_4.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_5.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_6.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_7.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_8.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_9.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_10.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_11.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_12.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_13.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_14.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_15.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_16.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_17.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_18.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_19.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_20.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_21.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_22.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_23.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_24.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_25.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_26.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_27.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_28.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 1.29,
                            "__threads": 1,
                            "__vmem_gb": 4.29,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-ud0d5b6c692/files/barcode_29.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/frag_bc_counts.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix_mex",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/generate_peak_matrix"
    },
    {
        "name": "MAKE_ATAC_SHARDS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "chunk": {
                                "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                "chemistry": null,
                                "gem_group": 1,
                                "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                "reads_interleaved": false,
                                "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                "subsample_rate": 1.0
                            },
                            "chunk_id": 0
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist_path",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-ud0d5b69fed/files/out.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "chunk_chemistry_map",
                            "type": "string[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": [
                                "3p;rev"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.json",
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "bch.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.bch.bincode",
                            "waiting": false
                        },
                        {
                            "id": "num_read_pairs",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": 299406391,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian make_atac_shards"
    },
    {
        "name": "MARK_ATAC_DUPLICATES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 3,
                    "__mem_gb": 7,
                    "__vmem_gb": 10
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 3314261674982909825,
                                    "five_p": {
                                        "contig_id": 0,
                                        "pos": 67605085
                                    },
                                    "three_p": {
                                        "contig_id": 0,
                                        "pos": 67605607
                                    }
                                },
                                "start": null
                            },
                            "unaligned_range": {
                                "end": 9983100,
                                "start": null
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 9957327168711179173,
                                    "five_p": {
                                        "contig_id": 0,
                                        "pos": 174364219
                                    },
                                    "three_p": {
                                        "contig_id": 0,
                                        "pos": 174364563
                                    }
                                },
                                "start": {
                                    "bc_hash": 3314261674982909825,
                                    "five_p": {
                                        "contig_id": 0,
                                        "pos": 67605085
                                    },
                                    "three_p": {
                                        "contig_id": 0,
                                        "pos": 67605607
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 19962920,
                                "start": 9983100
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 6496240892345969180,
                                    "five_p": {
                                        "contig_id": 1,
                                        "pos": 16477932
                                    },
                                    "three_p": {
                                        "contig_id": 1,
                                        "pos": 16478292
                                    }
                                },
                                "start": {
                                    "bc_hash": 9957327168711179173,
                                    "five_p": {
                                        "contig_id": 0,
                                        "pos": 174364219
                                    },
                                    "three_p": {
                                        "contig_id": 0,
                                        "pos": 174364563
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 29943670,
                                "start": 19962920
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 12558380101219272242,
                                    "five_p": {
                                        "contig_id": 1,
                                        "pos": 107906436
                                    },
                                    "three_p": {
                                        "contig_id": 1,
                                        "pos": 107906732
                                    }
                                },
                                "start": {
                                    "bc_hash": 6496240892345969180,
                                    "five_p": {
                                        "contig_id": 1,
                                        "pos": 16477932
                                    },
                                    "three_p": {
                                        "contig_id": 1,
                                        "pos": 16478292
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 39925190,
                                "start": 29943670
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 16396244603805718695,
                                    "five_p": {
                                        "contig_id": 2,
                                        "pos": 65399580
                                    },
                                    "three_p": {
                                        "contig_id": 2,
                                        "pos": 65400087
                                    }
                                },
                                "start": {
                                    "bc_hash": 12558380101219272242,
                                    "five_p": {
                                        "contig_id": 1,
                                        "pos": 107906436
                                    },
                                    "three_p": {
                                        "contig_id": 1,
                                        "pos": 107906732
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 49906291,
                                "start": 39925190
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 12165375036432386049,
                                    "five_p": {
                                        "contig_id": 3,
                                        "pos": 57330493
                                    },
                                    "three_p": {
                                        "contig_id": 3,
                                        "pos": 57330635
                                    }
                                },
                                "start": {
                                    "bc_hash": 16396244603805718695,
                                    "five_p": {
                                        "contig_id": 2,
                                        "pos": 65399580
                                    },
                                    "three_p": {
                                        "contig_id": 2,
                                        "pos": 65400087
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 59880183,
                                "start": 49906291
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 7698620154600720843,
                                    "five_p": {
                                        "contig_id": 4,
                                        "pos": 38461484
                                    },
                                    "three_p": {
                                        "contig_id": 4,
                                        "pos": 38462130
                                    }
                                },
                                "start": {
                                    "bc_hash": 12165375036432386049,
                                    "five_p": {
                                        "contig_id": 3,
                                        "pos": 57330493
                                    },
                                    "three_p": {
                                        "contig_id": 3,
                                        "pos": 57330635
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 69860909,
                                "start": 59880183
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 14463396655962498462,
                                    "five_p": {
                                        "contig_id": 5,
                                        "pos": 59281288
                                    },
                                    "three_p": {
                                        "contig_id": 5,
                                        "pos": 59281369
                                    }
                                },
                                "start": {
                                    "bc_hash": 7698620154600720843,
                                    "five_p": {
                                        "contig_id": 4,
                                        "pos": 38461484
                                    },
                                    "three_p": {
                                        "contig_id": 4,
                                        "pos": 38462130
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 79842001,
                                "start": 69860909
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 1963781554510403689,
                                    "five_p": {
                                        "contig_id": 6,
                                        "pos": 62452774
                                    },
                                    "three_p": {
                                        "contig_id": 6,
                                        "pos": 62453232
                                    }
                                },
                                "start": {
                                    "bc_hash": 14463396655962498462,
                                    "five_p": {
                                        "contig_id": 5,
                                        "pos": 59281288
                                    },
                                    "three_p": {
                                        "contig_id": 5,
                                        "pos": 59281369
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 89822649,
                                "start": 79842001
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 16736414225605563221,
                                    "five_p": {
                                        "contig_id": 7,
                                        "pos": 46400125
                                    },
                                    "three_p": {
                                        "contig_id": 7,
                                        "pos": 46400324
                                    }
                                },
                                "start": {
                                    "bc_hash": 1963781554510403689,
                                    "five_p": {
                                        "contig_id": 6,
                                        "pos": 62452774
                                    },
                                    "three_p": {
                                        "contig_id": 6,
                                        "pos": 62453232
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 99803758,
                                "start": 89822649
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 4703935553676114471,
                                    "five_p": {
                                        "contig_id": 8,
                                        "pos": 33182179
                                    },
                                    "three_p": {
                                        "contig_id": 8,
                                        "pos": 33182426
                                    }
                                },
                                "start": {
                                    "bc_hash": 16736414225605563221,
                                    "five_p": {
                                        "contig_id": 7,
                                        "pos": 46400125
                                    },
                                    "three_p": {
                                        "contig_id": 7,
                                        "pos": 46400324
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 109785486,
                                "start": 99803758
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 6375448501688766381,
                                    "five_p": {
                                        "contig_id": 9,
                                        "pos": 33591783
                                    },
                                    "three_p": {
                                        "contig_id": 9,
                                        "pos": 33592152
                                    }
                                },
                                "start": {
                                    "bc_hash": 4703935553676114471,
                                    "five_p": {
                                        "contig_id": 8,
                                        "pos": 33182179
                                    },
                                    "three_p": {
                                        "contig_id": 8,
                                        "pos": 33182426
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 119766413,
                                "start": 109785486
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 10,
                                        "pos": 38065488
                                    },
                                    "three_p": {
                                        "contig_id": 10,
                                        "pos": 38065576
                                    }
                                },
                                "start": {
                                    "bc_hash": 6375448501688766381,
                                    "five_p": {
                                        "contig_id": 9,
                                        "pos": 33591783
                                    },
                                    "three_p": {
                                        "contig_id": 9,
                                        "pos": 33592152
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 129748822,
                                "start": 119766413
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 442815639549770158,
                                    "five_p": {
                                        "contig_id": 11,
                                        "pos": 95186609
                                    },
                                    "three_p": {
                                        "contig_id": 11,
                                        "pos": 95187285
                                    }
                                },
                                "start": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 10,
                                        "pos": 38065488
                                    },
                                    "three_p": {
                                        "contig_id": 10,
                                        "pos": 38065576
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 139729539,
                                "start": 129748822
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 14035745171329273339,
                                    "five_p": {
                                        "contig_id": 11,
                                        "pos": 202281336
                                    },
                                    "three_p": {
                                        "contig_id": 11,
                                        "pos": 202281663
                                    }
                                },
                                "start": {
                                    "bc_hash": 442815639549770158,
                                    "five_p": {
                                        "contig_id": 11,
                                        "pos": 95186609
                                    },
                                    "three_p": {
                                        "contig_id": 11,
                                        "pos": 95187285
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 149710208,
                                "start": 139729539
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 12,
                                        "pos": 44301676
                                    },
                                    "three_p": {
                                        "contig_id": 12,
                                        "pos": 44302039
                                    }
                                },
                                "start": {
                                    "bc_hash": 14035745171329273339,
                                    "five_p": {
                                        "contig_id": 11,
                                        "pos": 202281336
                                    },
                                    "three_p": {
                                        "contig_id": 11,
                                        "pos": 202281663
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 159685856,
                                "start": 149710208
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 14,
                                        "pos": 27808113
                                    },
                                    "three_p": {
                                        "contig_id": 14,
                                        "pos": 27808280
                                    }
                                },
                                "start": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 12,
                                        "pos": 44301676
                                    },
                                    "three_p": {
                                        "contig_id": 12,
                                        "pos": 44302039
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 169665938,
                                "start": 159685856
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 15598269826006421685,
                                    "five_p": {
                                        "contig_id": 15,
                                        "pos": 60839041
                                    },
                                    "three_p": {
                                        "contig_id": 15,
                                        "pos": 60839300
                                    }
                                },
                                "start": {
                                    "bc_hash": 7475878434264988535,
                                    "five_p": {
                                        "contig_id": 14,
                                        "pos": 27808113
                                    },
                                    "three_p": {
                                        "contig_id": 14,
                                        "pos": 27808280
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 179645495,
                                "start": 169665938
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 13587446328253854420,
                                    "five_p": {
                                        "contig_id": 15,
                                        "pos": 171551120
                                    },
                                    "three_p": {
                                        "contig_id": 15,
                                        "pos": 171551259
                                    }
                                },
                                "start": {
                                    "bc_hash": 15598269826006421685,
                                    "five_p": {
                                        "contig_id": 15,
                                        "pos": 60839041
                                    },
                                    "three_p": {
                                        "contig_id": 15,
                                        "pos": 60839300
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 189626158,
                                "start": 179645495
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 8939351663642689122,
                                    "five_p": {
                                        "contig_id": 16,
                                        "pos": 69065371
                                    },
                                    "three_p": {
                                        "contig_id": 16,
                                        "pos": 69066037
                                    }
                                },
                                "start": {
                                    "bc_hash": 13587446328253854420,
                                    "five_p": {
                                        "contig_id": 15,
                                        "pos": 171551120
                                    },
                                    "three_p": {
                                        "contig_id": 15,
                                        "pos": 171551259
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 199608464,
                                "start": 189626158
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 5489169099974158821,
                                    "five_p": {
                                        "contig_id": 16,
                                        "pos": 187360824
                                    },
                                    "three_p": {
                                        "contig_id": 16,
                                        "pos": 187361234
                                    }
                                },
                                "start": {
                                    "bc_hash": 8939351663642689122,
                                    "five_p": {
                                        "contig_id": 16,
                                        "pos": 69065371
                                    },
                                    "three_p": {
                                        "contig_id": 16,
                                        "pos": 69066037
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 209589004,
                                "start": 199608464
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 5026523163957896722,
                                    "five_p": {
                                        "contig_id": 17,
                                        "pos": 101071476
                                    },
                                    "three_p": {
                                        "contig_id": 17,
                                        "pos": 101071689
                                    }
                                },
                                "start": {
                                    "bc_hash": 5489169099974158821,
                                    "five_p": {
                                        "contig_id": 16,
                                        "pos": 187360824
                                    },
                                    "three_p": {
                                        "contig_id": 16,
                                        "pos": 187361234
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 219571421,
                                "start": 209589004
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 13452153100524243086,
                                    "five_p": {
                                        "contig_id": 18,
                                        "pos": 47529821
                                    },
                                    "three_p": {
                                        "contig_id": 18,
                                        "pos": 47529897
                                    }
                                },
                                "start": {
                                    "bc_hash": 5026523163957896722,
                                    "five_p": {
                                        "contig_id": 17,
                                        "pos": 101071476
                                    },
                                    "three_p": {
                                        "contig_id": 17,
                                        "pos": 101071689
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 229550705,
                                "start": 219571421
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 15956816507038992360,
                                    "five_p": {
                                        "contig_id": 18,
                                        "pos": 158206895
                                    },
                                    "three_p": {
                                        "contig_id": 18,
                                        "pos": 158207174
                                    }
                                },
                                "start": {
                                    "bc_hash": 13452153100524243086,
                                    "five_p": {
                                        "contig_id": 18,
                                        "pos": 47529821
                                    },
                                    "three_p": {
                                        "contig_id": 18,
                                        "pos": 47529897
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 239532692,
                                "start": 229550705
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 8682387494168157188,
                                    "five_p": {
                                        "contig_id": 19,
                                        "pos": 76209477
                                    },
                                    "three_p": {
                                        "contig_id": 19,
                                        "pos": 76209732
                                    }
                                },
                                "start": {
                                    "bc_hash": 15956816507038992360,
                                    "five_p": {
                                        "contig_id": 18,
                                        "pos": 158206895
                                    },
                                    "three_p": {
                                        "contig_id": 18,
                                        "pos": 158207174
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 249513176,
                                "start": 239532692
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 521826667499838769,
                                    "five_p": {
                                        "contig_id": 20,
                                        "pos": 10726746
                                    },
                                    "three_p": {
                                        "contig_id": 20,
                                        "pos": 10726817
                                    }
                                },
                                "start": {
                                    "bc_hash": 8682387494168157188,
                                    "five_p": {
                                        "contig_id": 19,
                                        "pos": 76209477
                                    },
                                    "three_p": {
                                        "contig_id": 19,
                                        "pos": 76209732
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 259490597,
                                "start": 249513176
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 412583040319122649,
                                    "five_p": {
                                        "contig_id": 20,
                                        "pos": 118322338
                                    },
                                    "three_p": {
                                        "contig_id": 20,
                                        "pos": 118322783
                                    }
                                },
                                "start": {
                                    "bc_hash": 521826667499838769,
                                    "five_p": {
                                        "contig_id": 20,
                                        "pos": 10726746
                                    },
                                    "three_p": {
                                        "contig_id": 20,
                                        "pos": 10726817
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 269467797,
                                "start": 259490597
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 8586938483793928683,
                                    "five_p": {
                                        "contig_id": 21,
                                        "pos": 87995304
                                    },
                                    "three_p": {
                                        "contig_id": 21,
                                        "pos": 87995430
                                    }
                                },
                                "start": {
                                    "bc_hash": 412583040319122649,
                                    "five_p": {
                                        "contig_id": 20,
                                        "pos": 118322338
                                    },
                                    "three_p": {
                                        "contig_id": 20,
                                        "pos": 118322783
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 279448889,
                                "start": 269467797
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": {
                                    "bc_hash": 9532477467593839740,
                                    "five_p": {
                                        "contig_id": 22,
                                        "pos": 15112
                                    },
                                    "three_p": {
                                        "contig_id": 22,
                                        "pos": 15324
                                    }
                                },
                                "start": {
                                    "bc_hash": 8586938483793928683,
                                    "five_p": {
                                        "contig_id": 21,
                                        "pos": 87995304
                                    },
                                    "three_p": {
                                        "contig_id": 21,
                                        "pos": 87995430
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": 289430856,
                                "start": 279448889
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 2,
                            "__vmem_gb": 7,
                            "aligned_range": {
                                "end": null,
                                "start": {
                                    "bc_hash": 9532477467593839740,
                                    "five_p": {
                                        "contig_id": 22,
                                        "pos": 15112
                                    },
                                    "three_p": {
                                        "contig_id": 22,
                                        "pos": 15324
                                    }
                                }
                            },
                            "unaligned_range": {
                                "end": null,
                                "start": 289430856
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "aligned_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud0d5b6a421/files/aligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud0d5b6a421/files/aligned_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "unaligned_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud0d5b6a421/files/unaligned_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud0d5b6a421/files/unaligned_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "num_read_pairs",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": 299406391,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "bch.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud0d5b69fec/files/barcode_counts.bch.bincode",
                            "waiting": false
                        },
                        {
                            "id": "assay",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "arc",
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "deduped_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29-ud0d5b6c2af/files/deduped_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/frag_bc_counts.json",
                            "waiting": false
                        },
                        {
                            "id": "max_items_per_footprint",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": 5850,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian mark_atac_duplicates"
    },
    {
        "name": "WRITE_ATAC_BAM",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 0,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 0,
                                        "pos": 186154902
                                    }
                                },
                                "start": null
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 1,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 1,
                                        "pos": 129042239
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 0,
                                        "pos": 186154902
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 2,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 3,
                                        "pos": 52222752
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 1,
                                        "pos": 129042239
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 3,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 5,
                                        "pos": 62141180
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 3,
                                        "pos": 52222752
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 4,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 7,
                                        "pos": 58300206
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 5,
                                        "pos": 62141180
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 5,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 9,
                                        "pos": 61253472
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 7,
                                        "pos": 58300206
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 6,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 11,
                                        "pos": 94640968
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 9,
                                        "pos": 61253472
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 7,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 12,
                                        "pos": 50377101
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 11,
                                        "pos": 94640968
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 8,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 15,
                                        "pos": 83968701
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 12,
                                        "pos": 50377101
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 9,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 16,
                                        "pos": 103523253
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 15,
                                        "pos": 83968701
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 10,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 17,
                                        "pos": 142032013
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 16,
                                        "pos": 103523253
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 11,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 18,
                                        "pos": 168358826
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 17,
                                        "pos": 142032013
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 12,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 20,
                                        "pos": 30893142
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 18,
                                        "pos": 168358826
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 13,
                            "range": {
                                "end": {
                                    "pos": {
                                        "contig_id": 21,
                                        "pos": 120388039
                                    }
                                },
                                "start": {
                                    "pos": {
                                        "contig_id": 20,
                                        "pos": 30893142
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_id": 14,
                            "range": {
                                "end": null,
                                "start": {
                                    "pos": {
                                        "contig_id": 21,
                                        "pos": 120388039
                                    }
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "num_read_pairs",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                            "matchedFork": null,
                            "value": 299406391,
                            "waiting": false
                        },
                        {
                            "id": "deduped_shards",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28-ud0d5b6c2af/files/deduped_chunk.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29-ud0d5b6c2af/files/deduped_chunk.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "fastq_defs",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "max_items_per_footprint",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": 5850,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "possorted_bam",
                            "type": "bam",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam",
                            "waiting": false
                        },
                        {
                            "id": "possorted_bam_index",
                            "type": "bam.bai",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-ud0d5b6c567/files/possorted_bam.bam.bai",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian write_atac_bam"
    },
    {
        "name": "_PEAK_CALLER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "assay",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "arc",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "disable_bigwig",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "cut_sites",
                            "type": "bigwig",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-ud0d5b6c57b/files/cut_sites.bigwig",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "peak_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "CONVERT_SIGNAL_TRACK",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "cut_sites",
                            "type": "bedgraph",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/cut_sites.bedgraph",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "cut_sites",
                            "type": "bigwig",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-ud0d5b6c57b/files/cut_sites.bigwig",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/convert_signal_track"
    },
    {
        "name": "COUNT_CUT_SITES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 8,
                    "__vmem_gb": 11
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 4,
                            "__vmem_gb": 11
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "cut_sites",
                            "type": "bedgraph",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/cut_sites.bedgraph",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian count_cut_sites"
    },
    {
        "name": "DETECT_PEAKS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 5,
                    "__vmem_gb": 8
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr2"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr3"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr4"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr5"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr6"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr7"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chrX"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr8"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr9"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr11"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr10"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr12"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr13"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr14"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr15"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr16"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr17"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr18"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr20"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr19"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chrY",
                                "KI270713.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr22",
                                "KI270711.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "chr21",
                                "KI270726.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "KI270728.1",
                                "KI270721.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "KI270727.1",
                                "KI270731.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "GL000009.2",
                                "GL000218.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "GL000194.1",
                                "GL000213.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "GL000205.2",
                                "KI270734.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11,
                            "contigs": [
                                "GL000195.1",
                                "GL000219.1"
                            ],
                            "threshold": 15
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "assay",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "arc",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "cut_sites",
                            "type": "bedgraph",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/cut_sites.bedgraph",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        },
                        {
                            "id": "custom_peaks",
                            "type": "bed",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "peak_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/detect_peaks"
    },
    {
        "name": "_FASTQ_STAGER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "atac_sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "atac_barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "atac_subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "rna_chemistry",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "ARC-v1",
                            "waiting": false
                        },
                        {
                            "id": "rna_custom_chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "atac_chunks",
                            "type": "FastqDef[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "rna_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "rna_chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "atac_barcode_whitelist_path",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ATAC_SETUP_CHUNKS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "chunks",
                            "type": "FastqDef[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "read1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R1_001.fastq.gz",
                                    "read2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R3_001.fastq.gz",
                                    "reads_interleaved": false,
                                    "barcode": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_R2_001.fastq.gz",
                                    "sample_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq/samp26_S1_L002_I1_001.fastq.gz",
                                    "gem_group": 1,
                                    "subsample_rate": 1.0,
                                    "read_group": "samp26_CR_out:MissingLibrary:1:H5CK3DSX2:2",
                                    "chemistry": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ"
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist_path",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/setup_chunks"
    },
    {
        "name": "GEX_SETUP_CHUNKS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Gene Expression",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "chemistry_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "ARC-v1",
                            "waiting": false
                        },
                        {
                            "id": "custom_chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "default_library_type",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian setup_chunks"
    },
    {
        "name": "_GEX_CELLS_REPORTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "recovered_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1000,
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "slfe_feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "target_panel_summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "matrices_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "report_mol_inputs",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "matrix_computer_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "barcode_summary",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "filter_barcodes_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/per_barcode_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "multi_config_sha",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-ud0d5b6cd6e/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "molecule_info",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/molecule_info_non_multiplexed.h5",
                            "waiting": false
                        },
                        {
                            "id": "merged_subsampling_metrics",
                            "type": "pickle",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ud0d5b6ccaa/files/merged_metrics.pickle",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "SUBSAMPLE_READS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 6,
                    "__vmem_gb": 9
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "chunk_len": 8328544,
                            "chunk_start": 0,
                            "subsample_info": [
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 5000,
                                    "library_subsample_rates": [
                                        0.005310405978640494
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 10000,
                                    "library_subsample_rates": [
                                        0.010620811957280988
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 20000,
                                    "library_subsample_rates": [
                                        0.021241623914561976
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 30000,
                                    "library_subsample_rates": [
                                        0.03186243587184297
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 50000,
                                    "library_subsample_rates": [
                                        0.053104059786404936
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 94154,
                                    "library_subsample_rates": [
                                        0.0999991929025834
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 188309,
                                    "library_subsample_rates": [
                                        0.19999944788636256
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 282464,
                                    "library_subsample_rates": [
                                        0.29999970287014166
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 376619,
                                    "library_subsample_rates": [
                                        0.39999995785392084
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 470773,
                                    "library_subsample_rates": [
                                        0.4999991507565042
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 564928,
                                    "library_subsample_rates": [
                                        0.5999994057402833
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 659083,
                                    "library_subsample_rates": [
                                        0.6999996607240625
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 753238,
                                    "library_subsample_rates": [
                                        0.7999999157078417
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 847392,
                                    "library_subsample_rates": [
                                        0.899999108610425
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_rpc",
                                    "target_read_pairs_per_cell": 941547,
                                    "library_subsample_rates": [
                                        1.0
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 5000,
                                    "library_subsample_rates": [
                                        0.009100095394277774
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 10000,
                                    "library_subsample_rates": [
                                        0.01820019078855555
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 20000,
                                    "library_subsample_rates": [
                                        0.0364003815771111
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 30000,
                                    "library_subsample_rates": [
                                        0.05460057236566665
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 50000,
                                    "library_subsample_rates": [
                                        0.09100095394277775
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 54944,
                                    "library_subsample_rates": [
                                        0.09999912826863962
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 109888,
                                    "library_subsample_rates": [
                                        0.19999825653727923
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 164833,
                                    "library_subsample_rates": [
                                        0.2999992048249977
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 219777,
                                    "library_subsample_rates": [
                                        0.3999983330936373
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 274722,
                                    "library_subsample_rates": [
                                        0.49999928138135574
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 329666,
                                    "library_subsample_rates": [
                                        0.5999984096499954
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 384611,
                                    "library_subsample_rates": [
                                        0.6999993579377138
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 439555,
                                    "library_subsample_rates": [
                                        0.7999984862063535
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 494500,
                                    "library_subsample_rates": [
                                        0.8999994344940719
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc",
                                    "target_read_pairs_per_cell": 549444,
                                    "library_subsample_rates": [
                                        1.0
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 10000,
                                    "library_subsample_rates": [
                                        4.214607919555947e-05
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 50000,
                                    "library_subsample_rates": [
                                        0.00021073039597779736
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 100000,
                                    "library_subsample_rates": [
                                        0.0004214607919555947
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 250000,
                                    "library_subsample_rates": [
                                        0.0010536519798889869
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 500000,
                                    "library_subsample_rates": [
                                        0.0021073039597779737
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 1000000,
                                    "library_subsample_rates": [
                                        0.0042146079195559474
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 2500000,
                                    "library_subsample_rates": [
                                        0.010536519798889869
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 5000000,
                                    "library_subsample_rates": [
                                        0.021073039597779737
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 7500000,
                                    "library_subsample_rates": [
                                        0.0316095593966696
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 10000000,
                                    "library_subsample_rates": [
                                        0.042146079195559474
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 23726999,
                                    "library_subsample_rates": [
                                        0.09999999789269604
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 47453999,
                                    "library_subsample_rates": [
                                        0.2
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 50000000,
                                    "library_subsample_rates": [
                                        0.21073039597779736
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 71180998,
                                    "library_subsample_rates": [
                                        0.29999999789269605
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 94907998,
                                    "library_subsample_rates": [
                                        0.4
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 100000000,
                                    "library_subsample_rates": [
                                        0.4214607919555947
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 118634997,
                                    "library_subsample_rates": [
                                        0.49999999789269606
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 142361997,
                                    "library_subsample_rates": [
                                        0.6
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 166088996,
                                    "library_subsample_rates": [
                                        0.6999999978926961
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 189815996,
                                    "library_subsample_rates": [
                                        0.8
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 213542995,
                                    "library_subsample_rates": [
                                        0.899999997892696
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 237269995,
                                    "library_subsample_rates": [
                                        1.0
                                    ]
                                },
                                {
                                    "library_type": "Gene Expression",
                                    "subsample_type": "raw_reads",
                                    "target_read_pairs_per_cell": 1000000000,
                                    "library_subsample_rates": [
                                        0.0
                                    ]
                                }
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "molecule_info",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/molecule_info_non_multiplexed.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "target_mode",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ud0d5b6ccaa/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "merged_metrics",
                            "type": "pickle",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ud0d5b6ccaa/files/merged_metrics.pickle",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/subsample_reads"
    },
    {
        "name": "SUMMARIZE_BASIC_REPORTS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 3,
                    "__vmem_gb": 6
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrices_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/per_barcode_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "matrix_computer_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "barcode_summary",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                            "waiting": false
                        },
                        {
                            "id": "recovered_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1000,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "cell_bcs_only",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "summary_jsons",
                            "type": "json[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ud0d5b6ccaa/files/summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/non_multiplexed_summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/summary.json"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-ud0d5b6cd6e/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/summarize_basic_reports"
    },
    {
        "name": "WRITE_MOLECULE_INFO",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 16,
                    "__vmem_gb": 19
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 1,
                            "__vmem_gb": 19
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "counts_bc_order",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "target_panel_summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "matrix_computer_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "recovered_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1000,
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "filtered_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "multi_config_sha",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "sample_barcodes_json",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "per_sample_metrics",
                            "type": "SampleMetrics[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "single_mol_info",
                            "type": "SampleMoleculeInfo",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": {
                                "h5_file": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/molecule_info_non_multiplexed.h5",
                                "sample": "non_multiplexed",
                                "summary": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ud0d5b6cc91/files/non_multiplexed_summary.json"
                            },
                            "waiting": false
                        },
                        {
                            "id": "multi_mol_info",
                            "type": "SampleMoleculeInfo[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_molecule_info"
    },
    {
        "name": "_GEX_MATRIX_COMPUTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "barcodes_under_tissue",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "is_pd",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "libraries_to_translate",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [],
                            "waiting": false
                        },
                        {
                            "id": "chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "initial_reads",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "r1_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "r2_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "trim_polya_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "trim_tso_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_features",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "aligner",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "disable_target_umi_filter",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "rps_limit",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "write_bc_counts_json",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "slfe_feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_correction_csv",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud0d5b6b8be/files/barcode_summary.csv",
                            "waiting": false
                        },
                        {
                            "id": "barcode_summary",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_gene_bc_matrices_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "raw_gene_bc_matrices_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix",
                            "waiting": false
                        },
                        {
                            "id": "read_shards",
                            "type": "ReadShards",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "corrected_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                                ],
                                "invalid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                                ],
                                "valid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                                ]
                            },
                            "waiting": false
                        },
                        {
                            "id": "report_mol_inputs",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "annotation_files",
                            "type": "ann.bincode.lz4[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/per_barcode_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics_shard",
                            "type": "bmsf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/metrics_shard.bmsf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "bc_umi_info",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "bam_header",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud0d5b6b8be/files/bam_header",
                            "waiting": false
                        },
                        {
                            "id": "alignments",
                            "type": "asf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/pos_sorted.asf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "multi_metrics",
                            "type": "SampleMetrics[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "gem_well_alignment_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        },
                        {
                            "id": "sequencing_metrics",
                            "type": "smf.json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/sequencing_metrics.smf.json",
                            "waiting": false
                        },
                        {
                            "id": "bc_counts_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/bc_counts_json.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ALIGN_AND_COUNT",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 16,
                    "__vmem_gb": 19
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "AGTTATTTCTACTGCC",
                                    "valid": false
                                },
                                "start": null
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CCAACTTTCGTTCTTG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "AGTTATTTCTACTGCC",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CGTTTTTGATTAATGA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CCAACTTTCGTTCTTG",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GAGCATGCAGCTTGCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CGTTTTTGATTAATGA",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GGCCTTCATATATAAT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GAGCATGCAGCTTGCT",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GTGGTTAGCATGCATG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GGCCTTCATATATAAT",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TCCTTTAAGTTTCAGC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GTGGTTAGCATGCATG",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 4,
                            "__vmem_gb": 19,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TTTGGTTGATATCTTG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TCCTTTAAGTTTCAGC",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 21,
                            "__threads": 4,
                            "__vmem_gb": 24,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "ACCAAGTTCCTTAGGG",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TTTGGTTGATATCTTG",
                                    "valid": false
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 22,
                            "__threads": 4,
                            "__vmem_gb": 25,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "ATGACGAAGGTGAAAT",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "ACCAAGTTCCTTAGGG",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 21,
                            "__threads": 4,
                            "__vmem_gb": 24,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CCCAAACCAGCAACAG",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "ATGACGAAGGTGAAAT",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 21,
                            "__threads": 4,
                            "__vmem_gb": 24,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CTATAACCACCTAATG",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CCCAAACCAGCAACAG",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 22,
                            "__threads": 4,
                            "__vmem_gb": 25,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GGCCTTCGTTCACCAT",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CTATAACCACCTAATG",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 21,
                            "__threads": 4,
                            "__vmem_gb": 24,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TACCTCATCTGTTCAT",
                                    "valid": true
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GGCCTTCGTTCACCAT",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 22,
                            "__threads": 4,
                            "__vmem_gb": 25,
                            "range": {
                                "end": null,
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TACCTCATCTGTTCAT",
                                    "valid": true
                                }
                            },
                            "read_ann_subsample_rate": 0.2107303887605667
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "read_shards",
                            "type": "ReadShards",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "corrected_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                                ],
                                "invalid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                                ],
                                "valid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                                ]
                            },
                            "waiting": false
                        },
                        {
                            "id": "feature_counts",
                            "type": "fbc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/feature_counts.fbc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "target_set",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "aligner",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "aligner_subsample_rate",
                            "type": "float",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "is_pd",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "transcriptome_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 30,
                            "waiting": false
                        },
                        {
                            "id": "trim_polya_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "trim_tso_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "targeted_umi_min_read_count",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "total_barcode_counts",
                            "type": "tbcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/total_barcode_counts.tbcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_subset",
                            "type": "blf.json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "counts_bc_order",
                            "type": "csf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_sort.csf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "counts_feature_order",
                            "type": "csf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/feature_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/feature_sort.csf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "bc_umi_info",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "pos_sorted",
                            "type": "asf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/pos_sorted.asf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/pos_sorted.asf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "bam_header",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud0d5b6b8be/files/bam_header",
                            "waiting": false
                        },
                        {
                            "id": "barcode_summary",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ud0d5b6b8be/files/barcode_summary.csv",
                            "waiting": false
                        },
                        {
                            "id": "annotation_files",
                            "type": "ann.bincode.lz4[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_0.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_1.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_2.ann.bincode.lz4",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/read_annotations_3.ann.bincode.lz4"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "bmsf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/metrics_shard.bmsf"
                            ],
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian align_and_count"
    },
    {
        "name": "BARCODE_CORRECTION",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "AATGCATGTATGGATG",
                                    "valid": false
                                },
                                "start": null
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "ACCCGTAAGCAGCCCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "AATGCATGTATGGATG",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "ACTCGCGGCGGACCGC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "ACCCGTAAGCAGCCCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "AGGTAACCATCCCACA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "ACTCGCGGCGGACCGC",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "ATCAAGCTCACTAAAC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "AGGTAACCATCCCACA",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CAACCAGCATCCAGTT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "ATCAAGCTCACTAAAC",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CACTGTCCAGCTTTGC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CAACCAGCATCCAGTT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CATGCGGGTTTGGCGT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CACTGTCCAGCTTTGC",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CCCAGCGTATCAAATT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CATGCGGGTTTGGCGT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CCTCAGCATAAACCTT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CCCAGCGTATCAAATT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CGCCACACACAAAACT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CCTCAGCATAAACCTT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CTACAACAGGTTACAT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CGCCACACACAAAACT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CTGCCAGTAGCATATG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CTACAACAGGTTACAT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "CTTAACTGCGTAACTT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CTGCCAGTAGCATATG",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GAGCATGCAGCTTGCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "CTTAACTGCGTAACTT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GCACACAGGGTTATCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GAGCATGCAGCTTGCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GCCTGAGGCAAGTCTG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GCACACAGGGTTATCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GGAGCATATATTATTA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GCCTGAGGCAAGTCTG",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GGCTAATAGGACCGCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GGAGCATATATTATTA",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GGTCCGGGCATGGTGG",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GGCTAATAGGACCGCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GTACCTTTAACCTTTA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GGTCCGGGCATGGTGG",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "GTTACGCAACAAACAT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GTACCTTTAACCTTTA",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TAAAGGAAGGAGGTTA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "GTTACGCAACAAACAT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TATAGGTGTCCAGGGC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TAAAGGAAGGAGGTTA",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TCAGTAGGTGCATGGC",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TATAGGTGTCCAGGGC",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TCGGAGTCTCTTGGCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TCAGTAGGTGCATGGC",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TGACAAGTGTTAGCAA",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TCGGAGTCTCTTGGCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": {
                                    "gem_group": 1,
                                    "sequence": "TTACCTGGTTGATCCT",
                                    "valid": false
                                },
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TGACAAGTGTTAGCAA",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 4,
                            "__vmem_gb": 7,
                            "range": {
                                "end": null,
                                "start": {
                                    "gem_group": 1,
                                    "sequence": "TTACCTGGTTGATCCT",
                                    "valid": false
                                }
                            }
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/barcode_counts.bcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_segment_counts",
                            "type": "bsc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/barcode_segment_counts.bsc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "invalid_uncorrected",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/invalid.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "valid_read_metrics",
                            "type": "bcm.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/bc_correct_summary.bcm.bincode",
                            "waiting": false
                        },
                        {
                            "id": "libraries_to_translate",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "valid_corrected",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "invalid",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "corrected_barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/correct_barcode_counts.bcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "total_barcode_counts",
                            "type": "tbcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/total_barcode_counts.tbcc.bincode",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian barcode_correction"
    },
    {
        "name": "COLLATE_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 4,
                            "__vmem_gb": 4,
                            "sample": "non_multiplexed"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "per_barcode_metrics",
                            "type": "bmsf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/metrics_shard.bmsf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/metrics_shard.bmsf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "sample_barcodes_json",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "per_barcode_metrics",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/per_barcode_metrics.csv",
                            "waiting": false
                        },
                        {
                            "id": "per_lib_type_metrics",
                            "type": "map",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": {},
                            "waiting": false
                        },
                        {
                            "id": "multi_metrics",
                            "type": "SampleMetrics[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian collate_metrics"
    },
    {
        "name": "MAKE_READ_SHARDS_STRUCT",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "valid_reads",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "corrected_reads",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "invalid_reads",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "read_shards",
                            "type": "ReadShards",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "corrected_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                                ],
                                "invalid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                                ],
                                "valid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                                ]
                            },
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "MAKE_SHARD",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 2,
                            "__vmem_gb": 9,
                            "chunk_id": 0,
                            "feature_reference": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "r1_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "r2_length",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "subsample_rate",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "initial_read_pairs",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "target_features",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "target_set_name",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "feature_reference_path",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "libraries_to_translate",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [],
                            "waiting": false
                        },
                        {
                            "id": "write_bc_counts_json",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "valid",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "invalid",
                            "type": "shard[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/invalid.shard"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/barcode_counts.bcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_segment_counts",
                            "type": "bsc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/barcode_segment_counts.bsc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "feature_counts",
                            "type": "fbc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/feature_counts.fbc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "total_read_pairs",
                            "type": "int",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": 237269995,
                            "waiting": false
                        },
                        {
                            "id": "paired_end",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "bc_correct_summary",
                            "type": "bcm.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/bc_correct_summary.bcm.bincode",
                            "waiting": false
                        },
                        {
                            "id": "sequencing_metrics",
                            "type": "smf.json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/sequencing_metrics.smf.json",
                            "waiting": false
                        },
                        {
                            "id": "bc_counts_json",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/bc_counts_json.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian make_shard"
    },
    {
        "name": "MERGE_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "summaries",
                            "type": "json[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/summary.json",
                                null,
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ud0d5b6cc84/files/summary.json"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ud0d5b6cc86/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian merge_metrics"
    },
    {
        "name": "SET_ALIGNER_SUBSAMPLE_RATE",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 8,
                    "__vmem_gb": 11
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "rps_limit",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "barcodes_under_tissue",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "corrected_barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/correct_barcode_counts.bcc.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "aligner_subsample_rate",
                            "type": "float",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian set_aligner_subsample_rate"
    },
    {
        "name": "WRITE_BARCODE_INDEX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/correct_barcode_counts.bcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcodes_under_tissue",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_barcode_index"
    },
    {
        "name": "WRITE_BARCODE_SUMMARY",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "unique_gem_groups",
                            "type": "int[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                1
                            ],
                            "waiting": false
                        },
                        {
                            "id": "bc_umi_info",
                            "type": "bui[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_umi_info.bui",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_umi_info.bui"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "barcode_summary",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ud0d5b6cc83/files/barcode_summary.h5",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_barcode_summary"
    },
    {
        "name": "WRITE_H5_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 2,
                    "__vmem_gb": 5
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "counts",
                            "type": "csf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_sort.csf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_h5_matrix"
    },
    {
        "name": "WRITE_MATRIX_MARKET",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 2,
                    "__vmem_gb": 5
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "counts",
                            "type": "csf[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud0d5b6b8be/files/bc_sort.csf",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud0d5b6b8be/files/bc_sort.csf"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "barcode_index",
                            "type": "bi.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud0d5b6b8bd/files/barcode_index.bi.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "feature_bc_matrix",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_matrix_market"
    },
    {
        "name": "_SLFE_PARTIAL_FIRST_PASS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS",
        "state": "disabled",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "disabled",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0",
                    "names": [
                        "disabled",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "gem_well",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 1,
                            "waiting": false
                        },
                        {
                            "id": "read_chunks",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": [
                                {
                                    "chemistry": {
                                        "barcode": [
                                            {
                                                "kind": "gel_bead",
                                                "length": 16,
                                                "offset": 0,
                                                "read_type": "R1",
                                                "whitelist": "737K-arc-v1"
                                            }
                                        ],
                                        "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                        "endedness": "three_prime",
                                        "name": "ARC-v1",
                                        "rna": {
                                            "length": null,
                                            "min_length": null,
                                            "offset": 0,
                                            "read_type": "R2"
                                        },
                                        "rna2": null,
                                        "strandedness": "+",
                                        "umi": {
                                            "length": 12,
                                            "min_length": 10,
                                            "offset": 16,
                                            "read_type": "R1"
                                        }
                                    },
                                    "chunk_id": 0,
                                    "fastq_id": null,
                                    "fastqs": {
                                        "i1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I1_001.fastq.gz",
                                        "i2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_I2_001.fastq.gz",
                                        "r1": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R1_001.fastq.gz",
                                        "r1_interleaved": false,
                                        "r2": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scRNA/fastq/samp26_S2_L001_R2_001.fastq.gz"
                                    },
                                    "gem_group": 1,
                                    "library_id": 0,
                                    "library_type": "Gene Expression",
                                    "read_group": "samp26_CR_out:0:1:H5CWMDSX2:1",
                                    "read_lengths": {},
                                    "subsample_rate": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "read_shards",
                            "type": "ReadShards",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "corrected_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/valid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/valid_shard.shard"
                                ],
                                "invalid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-ud0d5b6b85a/files/invalid_shard.shard",
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-ud0d5b6b85a/files/invalid_shard.shard"
                                ],
                                "valid_reads": [
                                    "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-ud0d5b69ff2/files/valid.shard"
                                ]
                            },
                            "waiting": false
                        },
                        {
                            "id": "feature_counts",
                            "type": "fbc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ud0d5b69feb/files/feature_counts.fbc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "feature_reference",
                            "type": "frf.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud0d5b69feb/files/feature_reference.frf.bincode",
                            "waiting": false
                        },
                        {
                            "id": "target_set",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "chemistry_def",
                            "type": "ChemistryDef",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-arc-v1"
                                    }
                                ],
                                "description": "Single Cell Multiome ATAC + Gene Expression v1",
                                "endedness": "three_prime",
                                "name": "ARC-v1",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2"
                                },
                                "rna2": null,
                                "strandedness": "+",
                                "umi": {
                                    "length": 12,
                                    "min_length": 10,
                                    "offset": 16,
                                    "read_type": "R1"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "include_introns",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "aligner",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "is_pd",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        },
                        {
                            "id": "trim_polya_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "trim_tso_min_score",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 20,
                            "waiting": false
                        },
                        {
                            "id": "total_barcode_counts",
                            "type": "tbcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/total_barcode_counts.tbcc.bincode",
                            "waiting": false
                        },
                        {
                            "id": "corrected_barcode_counts",
                            "type": "bcc.bincode",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-ud0d5b6b85a/files/correct_barcode_counts.bcc.bincode",
                            "waiting": false
                        }
                    ],
                    "Return": null
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "_JOINT_CELL_DETECTOR",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "rna_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "rna_gem_groups",
                            "type": "int[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                1
                            ],
                            "waiting": false
                        },
                        {
                            "id": "disable_bc_multiplets",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "atac_cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-ud0d5b6cc91/files/merged_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "excluded_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        },
                        {
                            "id": "atac_singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-ud0d5b6cc91/files/atac_singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "rna_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "joint_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "joint_raw_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "joint_filtered_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_filtered_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "is_multi_genome",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "skip_analysis",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "DETECT_JOINT_CELL_BARCODES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 6,
                    "__vmem_gb": 9
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "rna_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "force_cells",
                            "type": "map\u003cMinCounts\u003e",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "atac_excluded_bcs",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "atac_formatted_cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/detect_joint_cell_barcodes"
    },
    {
        "name": "FILTER_PEAK_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 3,
                    "__vmem_gb": 6
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "num_analysis_bcs",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix_mex",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/filter_peak_matrix"
    },
    {
        "name": "FILTER_UMI_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "rna_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "gem_groups",
                            "type": "int[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                1
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "is_multi_genome",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/filter_umi_matrix"
    },
    {
        "name": "GENERATE_SC_ATAC_COUNTS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 6,
                    "__vmem_gb": 9
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr2"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr3"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr4"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr5"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr6"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr7"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chrX"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr8"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr9"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr11"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr10"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr12"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr13"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr14"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr15"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr16"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr17"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr18"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr20"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr19"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chrY",
                                "KI270713.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr22",
                                "KI270711.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "chr21",
                                "KI270726.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "KI270728.1",
                                "KI270721.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "KI270727.1",
                                "KI270731.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "GL000009.2",
                                "GL000218.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "GL000194.1",
                                "GL000213.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "GL000205.2",
                                "KI270734.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 6,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "contigs": [
                                "GL000195.1",
                                "GL000219.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "excluded_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "atac_singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-ud0d5b6cc91/files/atac_singlecell.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/generate_sc_atac_counts"
    },
    {
        "name": "MERGE_ATAC_RNA_MATRICES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "atac_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-ud0d5b6c692/files/raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "rna_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ud0d5b6cc83/files/raw_feature_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "rna_filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-ud0d5b6cc91/files/filtered_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS",
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "joint_raw_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "joint_raw_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_raw_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "joint_filtered_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/joint_filtered_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "skip_analysis",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/merge_atac_rna_matrices"
    },
    {
        "name": "MERGE_CELL_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "summary_jsons",
                            "type": "json[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/low_targeting_summary.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-ud0d5b6c6c4/files/gel_bead_doublet_summary.json",
                                null,
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/summary.json"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "merged_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-ud0d5b6cc91/files/merged_summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/merge_summary_metrics"
    },
    {
        "name": "MERGE_EXCLUDED_BARCODES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "barcode_exclusions",
                            "type": "json[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                null,
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-ud0d5b6c6c4/files/gel_bead_doublet_barcodes.json",
                                "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/low_targeting_barcodes.json"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "excluded_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/merge_excluded_barcodes"
    },
    {
        "name": "REMOVE_BARCODE_MULTIPLETS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS",
        "state": "disabled",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "disabled",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0",
                    "names": [
                        "disabled",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/barcode_counts.json",
                            "waiting": false
                        }
                    ],
                    "Return": null
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_barcode_multiplets"
    },
    {
        "name": "REMOVE_GEL_BEAD_DOUBLET_BARCODES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr2"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr3"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr4"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr5"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr6"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr7"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chrX"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr8"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr9"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr11"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr10"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr12"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr13"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr14"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr15"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr16"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr17"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr18"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr20"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr19"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chrY",
                                "KI270713.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr22",
                                "KI270711.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "chr21",
                                "KI270726.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "KI270728.1",
                                "KI270721.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "KI270727.1",
                                "KI270731.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "GL000009.2",
                                "GL000218.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "GL000194.1",
                                "GL000213.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "GL000205.2",
                                "KI270734.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "contigs": [
                                "GL000195.1",
                                "GL000219.1"
                            ],
                            "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-ud0d5b6c6c4/files/valid_barcodes.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/barcode_counts.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "gel_bead_doublet_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-ud0d5b6c6c4/files/gel_bead_doublet_barcodes.json",
                            "waiting": false
                        },
                        {
                            "id": "gel_bead_doublet_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-ud0d5b6c6c4/files/gel_bead_doublet_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "connect_matrix",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-ud0d5b6c6c4/files/connect_matrix.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_gel_bead_doublet_barcodes"
    },
    {
        "name": "REMOVE_LOW_TARGETING_BARCODES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr2"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr3"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr4"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr5"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr6"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr7"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chrX"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr8"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr9"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr11"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr10"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr12"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr13"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr14"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr15"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr16"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr17"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr18"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr20"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr19"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chrY",
                                "KI270713.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr22",
                                "KI270711.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "chr21",
                                "KI270726.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "KI270728.1",
                                "KI270721.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "KI270727.1",
                                "KI270731.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "GL000009.2",
                                "GL000218.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "GL000194.1",
                                "GL000213.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "GL000205.2",
                                "KI270734.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 2,
                            "__threads": 1,
                            "__vmem_gb": 5,
                            "contigs": [
                                "GL000195.1",
                                "GL000219.1"
                            ]
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "barcode_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/barcode_counts.json",
                            "waiting": false
                        },
                        {
                            "id": "low_targeting_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/low_targeting_barcodes.json",
                            "waiting": false
                        },
                        {
                            "id": "low_targeting_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/low_targeting_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "fragment_lengths",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/fragment_lengths.json",
                            "waiting": false
                        },
                        {
                            "id": "covered_bases",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-ud0d5b6c692/files/covered_bases.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_low_targeting_barcodes"
    },
    {
        "name": "_SC_ATAC_GEX_ANALYZER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "method",
                            "type": "AnalysisString",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "lsa",
                                "atac_gex": "pca",
                                "gex": "pca"
                            },
                            "waiting": false
                        },
                        {
                            "id": "projection_dims",
                            "type": "AnalysisInt",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": 15,
                                "atac_gex": 15,
                                "gex": 10
                            },
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage_max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "linkage_projection",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "analysis_csv",
                            "type": "AnalysisOutput",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "clustering": {
                                    "atac": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    },
                                    "gex": {
                                        "graphclust": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv"
                                        },
                                        "kmeans_2_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                        },
                                        "kmeans_3_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                        },
                                        "kmeans_4_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                        },
                                        "kmeans_5_clusters": {
                                            "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                                            "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                            "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                        }
                                    }
                                },
                                "dimensionality_reduction": {
                                    "atac": {
                                        "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                                        "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                                        "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                                        "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                                        "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_umap_csv/2_components/projection.csv"
                                    },
                                    "gex": {
                                        "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                                        "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                                        "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                                        "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                                        "pca_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/components.csv",
                                        "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                                        "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_umap_csv/2_components/projection.csv"
                                    }
                                },
                                "feature_linkage": {
                                    "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                    "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                                },
                                "tf_analysis": {
                                    "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                                    "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                                    "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "analysis_h5",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/analysis_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "peak_annotation",
                            "type": "tsv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "is_multi_genome",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "loupe_matrix_h5",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/loupe_matrix_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ATAC_GEX_SUMMARIZE_ANALYSIS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 5,
                    "__vmem_gb": 8
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "tf_propZ_matrix",
                            "type": "gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/tf_propZ_matrix.gz",
                            "waiting": false
                        },
                        {
                            "id": "peak_annotation",
                            "type": "tsv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutputMap",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "method": "lsa",
                                    "num_dims": 15,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                },
                                "atac_gex": null,
                                "gex": {
                                    "method": "pca",
                                    "num_dims": 10,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "tsne",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output"
                            },
                            "waiting": false
                        },
                        {
                            "id": "umap",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output"
                            },
                            "waiting": false
                        },
                        {
                            "id": "clustering",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering"
                            },
                            "waiting": false
                        },
                        {
                            "id": "differential_expression",
                            "type": "GexDeCluster",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "csv": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                                    "h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5"
                                },
                                "atac_gex": null,
                                "gex": {
                                    "csv": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                                    "h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "differential_accessibility",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis"
                            },
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "feature_linkage",
                            "type": "FeatureLinkageOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                            "matchedFork": null,
                            "value": {
                                "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                            },
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustering_output",
                            "type": "ClusteringOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "graphclust": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv"
                                    },
                                    "kmeans_2_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                    },
                                    "kmeans_3_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                    },
                                    "kmeans_4_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                    },
                                    "kmeans_5_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                    }
                                },
                                "gex": {
                                    "graphclust": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/graphclust/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv"
                                    },
                                    "kmeans_2_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv"
                                    },
                                    "kmeans_3_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv"
                                    },
                                    "kmeans_4_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv"
                                    },
                                    "kmeans_5_clusters": {
                                        "clusters": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                                        "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                                        "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv"
                                    }
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "dr_output",
                            "type": "DimensionReductionOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                                    "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                                    "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                                    "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                                    "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                                    "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                                    "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output/lsa_umap_csv/2_components/projection.csv"
                                },
                                "gex": {
                                    "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                                    "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                                    "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                                    "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                                    "pca_components": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/components.csv",
                                    "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                                    "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output/pca_umap_csv/2_components/projection.csv"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "analysis_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/analysis_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "loupe_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-ud0d5b6cdc3/files/loupe_matrix_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "is_multi_genome",
                            "type": "bool",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS",
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/analyzer/atac_gex_summarize_analysis"
    },
    {
        "name": "PARSE_REDUCED_DIM",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "linkage_projection",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutputMap",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "method": "lsa",
                                    "num_dims": 15,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                },
                                "atac_gex": null,
                                "gex": {
                                    "method": "pca",
                                    "num_dims": 10,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_dim_projection",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/analyzer/parse_reduced_dim"
    },
    {
        "name": "_ATAC_CLUSTERING_COMPUTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": {
                                "method": "lsa",
                                "num_dims": 15,
                                "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                            },
                            "waiting": false
                        },
                        {
                            "id": "matrix_clustering",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "neighbor_a",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_b",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "graphclust_neighbors",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_atac",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_gex",
                            "type": "GexDe",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "csv": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                                "h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5"
                            },
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ATAC_RUN_GRAPH_CLUSTERING",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 3,
                    "__vmem_gb": 6
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4,
                            "k_nearest": 58,
                            "method": "lsa",
                            "neighbor_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd05/files/neighbor_index_lsa.pickle",
                            "row_start": 0,
                            "submatrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd05/files/lsa_0_submatrix.h5",
                            "total_rows": 252,
                            "use_bcs": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd05/files/use_bcs.h5"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "num_neighbors",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_a",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_b",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "balltree_leaf_size",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "similarity_type",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "nn",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "chunked_neighbors",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "knn_clusters",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-ud0d5b6cd05/files/knn_clusters",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_graph_clustering"
    },
    {
        "name": "CLUSTER_CELLS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 3
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk2",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 5
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk3",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "minclusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 2,
                            "waiting": false
                        },
                        {
                            "id": "maxclusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustered_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-ud0d5b6cd05/files/clustered_data",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/cluster_cells"
    },
    {
        "name": "COMBINE_CLUSTERING",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "clustered_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-ud0d5b6cd05/files/clustered_data",
                            "waiting": false
                        },
                        {
                            "id": "knn_clusters",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-ud0d5b6cd05/files/knn_clusters",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        },
                        {
                            "id": "clustering_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_clustering.h5",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/combine_clustering"
    },
    {
        "name": "COMPUTE_DIFFERENTIAL_ATAC",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 0.7021484375,
                    "__vmem_gb": 3.7021484375
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "graphclust",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "graphclust",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "graphclust",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "graphclust",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_2_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_2_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 5,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "enrichment_analysis",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/perform_differential_analysis"
    },
    {
        "name": "COMPUTE_DIFFERENTIAL_GEX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "graphclust"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_2_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_3_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk2",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_4_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk3",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_5_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk4",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "clustering_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/lsa/lsa_clustering.h5",
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "is_antibody_only",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "skip",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "diffexp_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "diffexp_csv",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/analyzer/run_differential_expression"
    },
    {
        "name": "_DIMENSION_REDUCER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "method",
                            "type": "AnalysisString",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "lsa",
                                "atac_gex": "pca",
                                "gex": "pca"
                            },
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "projection_dims",
                            "type": "AnalysisInt",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": 15,
                                "atac_gex": 15,
                                "gex": 10
                            },
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutputMap",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": {
                                    "method": "lsa",
                                    "num_dims": 15,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                },
                                "atac_gex": null,
                                "gex": {
                                    "method": "pca",
                                    "num_dims": 10,
                                    "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                                }
                            },
                            "waiting": false
                        },
                        {
                            "id": "tsne",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output"
                            },
                            "waiting": false
                        },
                        {
                            "id": "umap",
                            "type": "AnalysisPath",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                                "atac_gex": null,
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output"
                            },
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "_ATAC_DIMENSION_REDUCER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "method",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "lsa",
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 15,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": {
                                "method": "lsa",
                                "num_dims": 15,
                                "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                            },
                            "waiting": false
                        },
                        {
                            "id": "tsne",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                            "waiting": false
                        },
                        {
                            "id": "umap",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "REDUCE_DIMENSIONS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "method": "lsa"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 15,
                            "waiting": false
                        },
                        {
                            "id": "num_bcs",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "num_features",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/reduce_dimensions"
    },
    {
        "name": "RUN_MANIFOLD_PROJECTION",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "method": "lsa",
                            "projection": "tsne",
                            "projection_dims": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 4,
                            "__vmem_gb": 9,
                            "method": "lsa",
                            "projection": "umap",
                            "projection_dims": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "params",
                            "type": "ManifoldParams",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "lsa"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "projections",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "tsne",
                                "umap"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "projection_output",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd05/files/projection_output",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_manifold_projection"
    },
    {
        "name": "_GEX_DIMENSION_REDUCER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "method",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "pca",
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 10,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": {
                                "method": "pca",
                                "num_dims": 10,
                                "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                            },
                            "waiting": false
                        },
                        {
                            "id": "tsne",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output",
                            "waiting": false
                        },
                        {
                            "id": "umap",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "REDUCE_DIMENSIONS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 10,
                            "waiting": false
                        },
                        {
                            "id": "num_bcs",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "num_features",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/reduce_dimensions"
    },
    {
        "name": "RUN_MANIFOLD_PROJECTION",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 9,
                            "method": "pca",
                            "projection": "tsne",
                            "projection_dims": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 4,
                            "__vmem_gb": 9,
                            "method": "pca",
                            "projection": "umap",
                            "projection_dims": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "params",
                            "type": "ManifoldParams",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "projections",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "tsne",
                                "umap"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "projection_output",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-ud0d5b6cd06/files/projection_output",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_manifold_projection"
    },
    {
        "name": "_FEATURE_LINKAGE_COMPUTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "merged_filtered_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_dim_projection",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_annotation",
                            "type": "tsv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "feature_linkage",
                            "type": "FeatureLinkageOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                            "matchedFork": null,
                            "value": {
                                "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "COMPUTE_FEATURE_LINKAGES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1.3251953125,
                    "__vmem_gb": 4.3251953125
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 58,
                            "chunk_start": 0
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 116,
                            "chunk_start": 58
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 174,
                            "chunk_start": 116
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 232,
                            "chunk_start": 174
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 290,
                            "chunk_start": 232
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 348,
                            "chunk_start": 290
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 406,
                            "chunk_start": 348
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 464,
                            "chunk_start": 406
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 522,
                            "chunk_start": 464
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 580,
                            "chunk_start": 522
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 638,
                            "chunk_start": 580
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 696,
                            "chunk_start": 638
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 754,
                            "chunk_start": 696
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 812,
                            "chunk_start": 754
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 870,
                            "chunk_start": 812
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 928,
                            "chunk_start": 870
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 986,
                            "chunk_start": 928
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 1044,
                            "chunk_start": 986
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1102,
                            "chunk_start": 1044
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 1160,
                            "chunk_start": 1102
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "__mem_gb": 2.14,
                            "__threads": 1,
                            "__vmem_gb": 5.14,
                            "chunk_end": 1218,
                            "chunk_start": 1160
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1276,
                            "chunk_start": 1218
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1334,
                            "chunk_start": 1276
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 23,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 1392,
                            "chunk_start": 1334
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk23",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 24,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1451,
                            "chunk_start": 1392
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk24",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 25,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1509,
                            "chunk_start": 1451
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk25",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 26,
                        "chunkDef": {
                            "__mem_gb": 2.13,
                            "__threads": 1,
                            "__vmem_gb": 5.13,
                            "chunk_end": 1567,
                            "chunk_start": 1509
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk26",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 27,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1625,
                            "chunk_start": 1567
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk27",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 28,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 1683,
                            "chunk_start": 1625
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk28",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 29,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1741,
                            "chunk_start": 1683
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk29",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 30,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 1799,
                            "chunk_start": 1741
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk30",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 31,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 1857,
                            "chunk_start": 1799
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk31",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 32,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 1915,
                            "chunk_start": 1857
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk32",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 33,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 1973,
                            "chunk_start": 1915
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk33",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 34,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2031,
                            "chunk_start": 1973
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk34",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 35,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2089,
                            "chunk_start": 2031
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk35",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 36,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2147,
                            "chunk_start": 2089
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk36",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 37,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2205,
                            "chunk_start": 2147
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk37",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 38,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2263,
                            "chunk_start": 2205
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk38",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 39,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2321,
                            "chunk_start": 2263
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk39",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 40,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2379,
                            "chunk_start": 2321
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk40",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 41,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2437,
                            "chunk_start": 2379
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk41",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 42,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2495,
                            "chunk_start": 2437
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk42",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 43,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2553,
                            "chunk_start": 2495
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk43",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 44,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2611,
                            "chunk_start": 2553
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk44",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 45,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2669,
                            "chunk_start": 2611
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk45",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 46,
                        "chunkDef": {
                            "__mem_gb": 2.12,
                            "__threads": 1,
                            "__vmem_gb": 5.12,
                            "chunk_end": 2727,
                            "chunk_start": 2669
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk46",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 47,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2785,
                            "chunk_start": 2727
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk47",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 48,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2843,
                            "chunk_start": 2785
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk48",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 49,
                        "chunkDef": {
                            "__mem_gb": 2.11,
                            "__threads": 1,
                            "__vmem_gb": 5.11,
                            "chunk_end": 2902,
                            "chunk_start": 2843
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk49",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "merged_filtered_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "atac_peak_annotation",
                            "type": "tsv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_metadata",
                            "type": "BarcodeMetadata",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
                            "matchedFork": null,
                            "value": {
                                "smoothing_weights": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/smoothing_weights.h5",
                                "similarity_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/similarity_matrix.h5",
                                "depth_scale_factors": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/depth_scale_factors.csv"
                            },
                            "waiting": false
                        },
                        {
                            "id": "feature_grouping",
                            "type": "pkl",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/feature_grouping.pkl",
                            "waiting": false
                        },
                        {
                            "id": "max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "feature_linkage",
                            "type": "FeatureLinkageOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                            "matchedFork": null,
                            "value": {
                                "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage.bedpe",
                                "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/feature_linkage_matrix.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-ud0d5b6cd21/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/feature_linkage/compute_feature_linkages"
    },
    {
        "name": "PREPROCESS_JOINT_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 2,
                    "__vmem_gb": 5
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "merged_filtered_matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_dim_projection",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "max_dist_mb",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "barcode_metadata",
                            "type": "BarcodeMetadata",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
                            "matchedFork": null,
                            "value": {
                                "smoothing_weights": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/smoothing_weights.h5",
                                "similarity_matrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/similarity_matrix.h5",
                                "depth_scale_factors": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/depth_scale_factors.csv"
                            },
                            "waiting": false
                        },
                        {
                            "id": "feature_grouping",
                            "type": "pkl",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-ud0d5b6cd09/files/feature_grouping.pkl",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/feature_linkage/preprocess_joint_matrix"
    },
    {
        "name": "_GEX_CLUSTERING_COMPUTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reduced_data",
                            "type": "ProjectionOutput",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": {
                                "method": "pca",
                                "num_dims": 10,
                                "projection": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data"
                            },
                            "waiting": false
                        },
                        {
                            "id": "matrix_clustering",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "matrix",
                            "type": "AnalysisH5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": {
                                "atac": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                                "gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                                "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac_gex.h5"
                            },
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "neighbor_a",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_b",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "graphclust_neighbors",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_atac",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_gex",
                            "type": "GexDe",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": {
                                "csv": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                                "h5": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5"
                            },
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ATAC_RUN_GRAPH_CLUSTERING",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 3,
                    "__vmem_gb": 6
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4,
                            "k_nearest": 58,
                            "method": "pca",
                            "neighbor_index": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd06/files/neighbor_index_pca.pickle",
                            "row_start": 0,
                            "submatrix": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd06/files/pca_0_submatrix.h5",
                            "total_rows": 252,
                            "use_bcs": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-ud0d5b6cd06/files/use_bcs.h5"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "num_neighbors",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_a",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "neighbor_b",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "balltree_leaf_size",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "similarity_type",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "nn",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "chunked_neighbors",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "knn_clusters",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-ud0d5b6cd06/files/knn_clusters",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_graph_clustering"
    },
    {
        "name": "CLUSTER_CELLS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 2
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 3
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk2",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 5,
                            "__threads": 1,
                            "__vmem_gb": 8,
                            "n_clusters": 5
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk3",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "reduced_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-ud0d5b6ccfc/files/reduced_data",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "minclusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": 2,
                            "waiting": false
                        },
                        {
                            "id": "maxclusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "num_dims",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustered_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-ud0d5b6cd06/files/clustered_data",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/cluster_cells"
    },
    {
        "name": "COMBINE_CLUSTERING",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "clustered_data",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-ud0d5b6cd06/files/clustered_data",
                            "waiting": false
                        },
                        {
                            "id": "knn_clusters",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-ud0d5b6cd06/files/knn_clusters",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        },
                        {
                            "id": "clustering_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_clustering.h5",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/combine_clustering"
    },
    {
        "name": "COMPUTE_DIFFERENTIAL_ATAC",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 0.7021484375,
                    "__vmem_gb": 3.7021484375
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "graphclust",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "graphclust",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "graphclust",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "graphclust",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_2_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_2_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_3_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "kmeans_4_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 1,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 2,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 3,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 4,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 0.757,
                            "__threads": 4,
                            "__vmem_gb": 3.76,
                            "cluster": 5,
                            "clustering_key": "kmeans_5_clusters",
                            "method": "pca"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "factorization",
                            "type": "string[]",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": [
                                "pca"
                            ],
                            "waiting": false
                        },
                        {
                            "id": "clustering",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "enrichment_analysis",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-ud0d5b6cdaa/files/enrichment_analysis",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/perform_differential_analysis"
    },
    {
        "name": "COMPUTE_DIFFERENTIAL_GEX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "graphclust"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_2_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk1",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_3_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk2",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_4_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk3",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 3,
                            "__threads": 1,
                            "__vmem_gb": 6,
                            "clustering_key": "kmeans_5_clusters"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk4",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "matrix_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/gex.h5",
                            "waiting": false
                        },
                        {
                            "id": "clustering_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-ud0d5b6cd11/files/clustering/pca/pca_clustering.h5",
                            "waiting": false
                        },
                        {
                            "id": "random_seed",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "max_clusters",
                            "type": "int",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "is_antibody_only",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "skip",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "diffexp_h5",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_h5.h5",
                            "waiting": false
                        },
                        {
                            "id": "diffexp_csv",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-ud0d5b6cd12/files/diffexp_csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/analyzer/run_differential_expression"
    },
    {
        "name": "_PEAK_ANNOTATOR",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "pwm_threshold",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "tf_propZ_matrix",
                            "type": "gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/tf_propZ_matrix.gz",
                            "waiting": false
                        },
                        {
                            "id": "peak_annotation",
                            "type": "tsv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        },
                        {
                            "id": "peak_motif_hits",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "ANNOTATE_PEAKS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 5,
                    "__vmem_gb": 8
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 1002,
                            "chunk_start": 0,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 2005,
                            "chunk_start": 1002,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 3007,
                            "chunk_start": 2005,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 4010,
                            "chunk_start": 3007,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 5012,
                            "chunk_start": 4010,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 6015,
                            "chunk_start": 5012,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 7017,
                            "chunk_start": 6015,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 8020,
                            "chunk_start": 7017,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 9022,
                            "chunk_start": 8020,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 10025,
                            "chunk_start": 9022,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 11028,
                            "chunk_start": 10025,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 12030,
                            "chunk_start": 11028,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 13033,
                            "chunk_start": 12030,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 14035,
                            "chunk_start": 13033,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 15038,
                            "chunk_start": 14035,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 16040,
                            "chunk_start": 15038,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 17043,
                            "chunk_start": 16040,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 18045,
                            "chunk_start": 17043,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 19048,
                            "chunk_start": 18045,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "chunk_end": 20051,
                            "chunk_start": 19048,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "peak_annotation",
                            "type": "tsv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-ud0d5b6ccfc/files/peak_annotation.tsv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/annotate_peaks"
    },
    {
        "name": "COMPUTE_GC_DISTRIBUTION",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "GCdict",
                            "type": "pickle",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join-ud0d5b6ccfc/files/GCdict.pickle",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/compute_gc_dist"
    },
    {
        "name": "GENERATE_TF_MATRIX",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 3,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "filtered_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "peak_motif_hits",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "filtered_tf_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix.h5",
                            "waiting": false
                        },
                        {
                            "id": "filtered_tf_bc_matrix_mex",
                            "type": "path",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/filtered_tf_bc_matrix_mex",
                            "waiting": false
                        },
                        {
                            "id": "tf_propZ_matrix",
                            "type": "gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-ud0d5b6cda2/files/tf_propZ_matrix.gz",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/generate_tf_matrix"
    },
    {
        "name": "SCAN_MOTIFS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.22130177514792898_0.39447513812154694",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.39447513812154694_0.4158291457286432",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.4158291457286432_0.4317617866004963",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.4317617866004963_0.44627192982456143",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.44627192982456143_0.4588100686498856",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.4588100686498856_0.47162162162162163",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.47162162162162163_0.484472049689441",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.484472049689441_0.49777777777777776",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.49777777777777776_0.5117021276595745",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5117021276595745_0.5266666666666666",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5266666666666666_0.5423162583518931",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5423162583518931_0.5572519083969466",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5572519083969466_0.5722543352601156",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5722543352601156_0.5868544600938967",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5868544600938967_0.5997506234413965",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.5997506234413965_0.6133333333333333",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6133333333333333_0.6266996291718171",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6266996291718171_0.6402173913043478",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6402173913043478_0.6534148827726809",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6534148827726809_0.6670341786108048",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 20,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6670341786108048_0.6823529411764706",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk20",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 21,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6823529411764706_0.6984318455971049",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk21",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 22,
                        "chunkDef": {
                            "GCdict": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-ud0d5b6cd18/files/GCdict_0.6984318455971049_0.8481012658227848",
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 13,
                            "skip": false
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk22",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "globalGCdict",
                            "type": "pickle",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join-ud0d5b6ccfc/files/GCdict.pickle",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "pwm_threshold",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "peak_motif_hits",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-ud0d5b6cd18/files/peak_motif_hits.bed",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/scan_motifs"
    },
    {
        "name": "_SC_ATAC_METRIC_COLLECTOR",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "basic_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_mapping",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_cells",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-ud0d5b6cc91/files/atac_singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/frag_bc_counts.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "singlecell_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6ccec/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-ud0d5b6c6e2/files/summary_metrics.json",
                            "waiting": false
                        },
                        {
                            "id": "insert_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-ud0d5b6c567/files/insert_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "bulk_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/bulk_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/singlecell_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "complexity_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/complexity_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "tss_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv",
                            "waiting": false
                        },
                        {
                            "id": "ctcf_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "COMPUTE_FRAGMENT_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 4,
                    "__mem_gb": 3,
                    "__vmem_gb": 6
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "fragments_index",
                            "type": "tsv.gz.tbi",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz.tbi",
                            "waiting": false
                        },
                        {
                            "id": "peaks",
                            "type": "bed",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peaks.bed",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "targeting_only",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": true,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "ctcf_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                            "waiting": false
                        },
                        {
                            "id": "tss_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/frag_bc_counts.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS"
            }
        ],
        "stagecodeLang": "Compiled",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian compute_fragment_metrics"
    },
    {
        "name": "ESTIMATE_LIBRARY_COMPLEXITY",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 8,
                    "__vmem_gb": 11
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "jobinfo",
                        "log",
                        "stage_defs",
                        "stderr",
                        "stdout"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "chunk_outs",
                        "complete",
                        "jobinfo",
                        "log",
                        "outs",
                        "stderr",
                        "stdout"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_0.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk00",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 1,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_1.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk01",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 2,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_2.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk02",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 3,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_3.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk03",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 4,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_4.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk04",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 5,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_5.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk05",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 6,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_6.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk06",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 7,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_7.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk07",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 8,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_8.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk08",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 9,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_9.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk09",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 10,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_10.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk10",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 11,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_11.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk11",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 12,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_12.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk12",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 13,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_13.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk13",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 14,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_14.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk14",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 15,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_15.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk15",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 16,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_16.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk16",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 17,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_17.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk17",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 18,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_18.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk18",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    },
                    {
                        "index": 19,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7,
                            "barcodes": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-ud0d5b6cc91/files/barcode_19.txt"
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk19",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sequencing_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "fragments",
                            "type": "tsv.gz",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/fragments.tsv.gz",
                            "waiting": false
                        },
                        {
                            "id": "cell_barcodes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-ud0d5b6cc85/files/atac_formatted_cell_barcodes.csv",
                            "waiting": false
                        },
                        {
                            "id": "frag_bc_counts",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/frag_bc_counts.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "bulk_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/bulk_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "complexity_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/complexity_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/singlecell_complexity.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/estimate_library_complexity"
    },
    {
        "name": "MERGE_SINGLECELL_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 8,
                    "__vmem_gb": 11
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 8,
                            "__threads": 1,
                            "__vmem_gb": 11
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_mapping",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_cells",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-ud0d5b6cc91/files/atac_singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_targets",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/singlecell.csv",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/merge_singlecell_metrics"
    },
    {
        "name": "REPORT_INSERT_SIZES",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "insert_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-ud0d5b6c567/files/insert_summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/report_insert_sizes"
    },
    {
        "name": "REPORT_TSS_CTCF",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 1,
                    "__vmem_gb": 4
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 1,
                            "__threads": 1,
                            "__vmem_gb": 4
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "tss_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv",
                            "waiting": false
                        },
                        {
                            "id": "ctcf_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary_metrics",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-ud0d5b6c6e2/files/summary_metrics.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/report_tss_ctcf"
    },
    {
        "name": "SUMMARIZE_SINGLECELL_METRICS",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6ccec/files/summary.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/summarize_singlecell_metrics"
    },
    {
        "name": "_SC_ATAC_REPORTER",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER",
        "type": "pipeline",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": null,
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0/split",
                    "names": []
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0/join",
                    "names": []
                },
                "chunks": [],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "peak_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                            "waiting": false
                        },
                        {
                            "id": "cell_calling_summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "filtered_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "excluded_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        },
                        {
                            "id": "bulk_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/bulk_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/singlecell_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "complexity_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/complexity_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "basic_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6ccec/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "insert_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-ud0d5b6c567/files/insert_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "tss_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv",
                            "waiting": false
                        },
                        {
                            "id": "ctcf_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                            "waiting": false
                        },
                        {
                            "id": "sc_insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-ud0d5b6c6e2/files/summary_metrics.json",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        },
                        {
                            "id": "analysis",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "web_summary",
                            "type": "html",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-ud0d5b6cd0c/files/web_summary.html",
                            "waiting": false
                        },
                        {
                            "id": "ws_data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-ud0d5b6cd0c/files/data.json",
                            "waiting": false
                        },
                        {
                            "id": "summary_csv",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary_csv.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER"
            }
        ],
        "stagecodeLang": "",
        "stagecodeCmd": ""
    },
    {
        "name": "CREATE_WEBSUMMARY",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 16,
                    "__vmem_gb": 19
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 16,
                            "__threads": 1,
                            "__vmem_gb": 19
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "barcode_whitelist",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "737K-arc-v1",
                            "waiting": false
                        },
                        {
                            "id": "singlecell",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6cce2/files/singlecell.csv",
                            "waiting": false
                        },
                        {
                            "id": "tss_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/tss.csv",
                            "waiting": false
                        },
                        {
                            "id": "ctcf_relpos",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-ud0d5b6c692/files/ctcf.csv",
                            "waiting": false
                        },
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_desc",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "sample_def",
                            "type": "map[]",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                            "matchedFork": null,
                            "value": [
                                {
                                    "fastq_id": null,
                                    "fastq_mode": "ILMN_BCL2FASTQ",
                                    "gem_group": null,
                                    "lanes": null,
                                    "library_type": "Chromatin Accessibility",
                                    "read_path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/scATAC/fastq",
                                    "sample_indices": [
                                        "any"
                                    ],
                                    "sample_names": [
                                        "samp26"
                                    ],
                                    "subsample_rate": null,
                                    "target_set": null,
                                    "target_set_name": null
                                }
                            ],
                            "waiting": false
                        },
                        {
                            "id": "insert_sizes",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/insert_sizes.csv",
                            "waiting": false
                        },
                        {
                            "id": "summary_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "bulk_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/bulk_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_complexity",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/singlecell_complexity.json",
                            "waiting": false
                        },
                        {
                            "id": "analysis",
                            "type": "h5",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "filtered_peak_bc_matrix",
                            "type": "h5",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-ud0d5b6cca6/files/atac.h5",
                            "waiting": false
                        },
                        {
                            "id": "excluded_barcodes",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-ud0d5b6c6e0/files/excluded_barcodes.json",
                            "waiting": false
                        },
                        {
                            "id": "count_dict",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud0d5b6c567/files/count_dict.json",
                            "waiting": false
                        },
                        {
                            "id": "debug",
                            "type": "bool",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": false,
                            "waiting": false
                        },
                        {
                            "id": "peak_qval",
                            "type": "float",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "web_summary",
                            "type": "html",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-ud0d5b6cd0c/files/web_summary.html",
                            "waiting": false
                        },
                        {
                            "id": "data",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-ud0d5b6cd0c/files/data.json",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/reporter/create_websummary"
    },
    {
        "name": "SUMMARIZE_REPORTS_SINGLECELL",
        "fqname": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
        "type": "stage",
        "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL",
        "state": "complete",
        "metadata": {
            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL",
            "names": []
        },
        "forks": [
            {
                "index": 0,
                "argPermute": null,
                "joinDef": {
                    "__threads": 1,
                    "__mem_gb": 4,
                    "__vmem_gb": 7
                },
                "state": "complete",
                "metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0",
                    "names": [
                        "complete",
                        "invocation",
                        "outs",
                        "vdrkill"
                    ]
                },
                "split_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/split",
                    "names": [
                        "args",
                        "complete",
                        "stage_defs"
                    ]
                },
                "join_metadata": {
                    "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/join",
                    "names": [
                        "args",
                        "chunk_defs",
                        "complete",
                        "outs"
                    ]
                },
                "chunks": [
                    {
                        "index": 0,
                        "chunkDef": {
                            "__mem_gb": 4,
                            "__threads": 1,
                            "__vmem_gb": 7
                        },
                        "state": "complete",
                        "metadata": {
                            "path": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0",
                            "names": [
                                "args",
                                "complete",
                                "jobinfo",
                                "log",
                                "outs",
                                "stderr",
                                "stdout"
                            ]
                        }
                    }
                ],
                "bindings": {
                    "Argument": [
                        {
                            "id": "sample_id",
                            "type": "string",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "samp26_CR_out",
                            "waiting": false
                        },
                        {
                            "id": "reference_path",
                            "type": "path",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
                            "waiting": false
                        },
                        {
                            "id": "complexity_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-ud0d5b6cc91/files/complexity_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "cell_calling_summary",
                            "type": "json",
                            "mode": "",
                            "node": null,
                            "matchedFork": null,
                            "value": null,
                            "waiting": false
                        },
                        {
                            "id": "peak_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-ud0d5b6c57b/files/peak_metrics.json",
                            "waiting": false
                        },
                        {
                            "id": "basic_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud0d5b6c2af/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "insert_summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-ud0d5b6c567/files/insert_summary.json",
                            "waiting": false
                        },
                        {
                            "id": "singlecell_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-ud0d5b6ccec/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "enrichment_results",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-ud0d5b6c6e2/files/summary_metrics.json",
                            "waiting": false
                        }
                    ],
                    "Return": [
                        {
                            "id": "analysis_params",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/analysis_params.json",
                            "waiting": false
                        },
                        {
                            "id": "summary",
                            "type": "json",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary.json",
                            "waiting": false
                        },
                        {
                            "id": "summary_csv",
                            "type": "csv",
                            "mode": "reference",
                            "node": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL",
                            "matchedFork": null,
                            "value": "/srv/scratch/ekotler/scMultiomics/samp26_20210520/samp26_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-ud0d5b6cd0a/files/summary_csv.csv",
                            "waiting": false
                        }
                    ]
                }
            }
        ],
        "edges": [
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL"
            },
            {
                "from": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR",
                "to": "ID.samp26_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL"
            }
        ],
        "stagecodeLang": "Python",
        "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/reporter/summarize_reports_singlecell"
    }
]