@include "rna/_sc_rna_analyzer_stages.mro"

call SUMMARIZE_ANALYSIS(
    matrix_h5                     = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u78ffd1aff0/files/preprocessed_matrix_h5.h5",
    pca_h5                        = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u78ffd1affa/files/pca_h5.h5",
    clustering_h5                 = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u78ffd1b060/files/clustering_h5.h5",
    diffexp_h5                    = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u78ffd1b061/files/diffexp_h5.h5",
    tsne_h5                       = null,
    umap_h5                       = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u78ffd1b008/files/umap_h5.h5",
    pca_csv                       = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u78ffd1affa/files/pca_csv",
    clustering_csv                = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u78ffd1b060/files/clustering_csv",
    diffexp_csv                   = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u78ffd1b061/files/diffexp_csv",
    tsne_csv                      = null,
    umap_csv                      = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u78ffd1b008/files/umap_csv",
    multi_genome_summary          = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u78ffd1aff9/files/multi_genome_summary.json",
    multi_genome_csv              = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u78ffd1aff9/files/multi_genome_csv",
    multi_genome_json             = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-aggr-Aiptasia/SC_RNA_AGGREGATOR_CS/COUNT_AGGR/SC_RNA_AGGREGATOR/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u78ffd1aff9/files/multi_genome_json",
    is_multi_genome               = false,
    chemistry_batch_correction    = false,
    batch_score_before_correction = null,
    batch_score_after_correction  = null,
)
