@include "_make_fastqs_stages.mro"

call MAKE_FASTQS_PREFLIGHT_LOCAL(
    run_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/BCL/",
    check_executables = false,
    lanes = null,
    specs = [
        {
            "csv": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172_v2.csv"
        }
    ],
    bcl2fastq2_args = " -p 6 -d 6 -r 6 -w 6 --barcode-mismatches 1",
    barcode_whitelist = "/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/737K-august-2016.txt,/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz",
    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,
    bases_mask = null,
    ignore_dual_index = false,
    all_mkfastq_args = "--id=G172_Run2_unlane --run=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/BCL/ --csv=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172_v2.csv",
)