@include "rna/_common_stages.mro"

call CELLRANGER_PREFLIGHT(
    full_check        = true,
    chemistry         = "auto",
    sample_def        = [
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1",
            "sample_indices": ["any"],
            "sample_names": ["Peak_004_2reprep"],
            "subsample_rate": null,
        },
    ],
    target_set        = null,
    reference_path    = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    feature_reference = null,
    recovered_cells   = {
        per_gem_well: null,
        per_sample:   null,
    },
    force_cells       = {
        per_gem_well: null,
        per_sample:   null,
    },
    r1_length         = null,
    r2_length         = null,
    targeting_method  = null,
)
