@include "make_fastqs_cs.mro"

call MAKE_FASTQS_CS(
    run_path              = "/gpfs/data/yanailab/runs/2021-10-14/bcl",
    lanes                 = null,
    specs                 = [{
        "csv": "/gpfs/data/yanailab/runs/2021-10-14/invivopilot.csv"
    }],
    project               = "H3GY2AFX3",
    bases_mask            = null,
    barcode_whitelist     = "/gpfs/data/yanailab/projects/db3562/10x/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/737K-august-2016.txt,/gpfs/data/yanailab/projects/db3562/10x/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz",
    bcl2fastq1_args       = " --mismatches=1",
    bcl2fastq2_args       = " -p 6 -d 6 -r 6 -w 6 --barcode-mismatches 1",
    bc_read_type          = "R1",
    bc_start_index        = 0,
    bc_length             = 16,
    si_read_type          = "I1",
    umi_read_type         = "R1",
    umi_start_index       = 16,
    umi_length            = 10,
    output_path           = null,
    interop_output_path   = null,
    delete_undetermined   = false,
    ignore_dual_index     = true,
    run_qc                = false,
    max_bcl2fastq_threads = 6,
    software_version      = "cellranger 3.1.0",
    all_mkfastq_args      = "--id=invivopilot --run=/gpfs/data/yanailab/runs/2021-10-14/bcl --samplesheet=invivopilot.csv --ignore-dual-index",
)