@include "_basic_sc_rna_counter_stages.mro"

call COUNT_GENES(
    sample_id = "Chow_1_Test",
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u8c0aa71e9d/files/alignments.bam"
    ],
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    feature_reference = null,
    chemistry_def = {
        "si_read_offset": 0,
        "strandedness": "+",
        "umi_read_offset": 16,
        "barcode_read_type": "R1",
        "umi_read_type": "R1",
        "barcode_read_length": 16,
        "rna_read_type": "R2",
        "barcode_whitelist": "737K-august-2016",
        "si_read_type": "I1",
        "rna_read_length": null,
        "description": "Single Cell 3' v2",
        "rna_read_offset": 0,
        "barcode_read_offset": 0,
        "rna_read2_type": null,
        "endedness": "three_prime",
        "name": "SC3Pv2",
        "umi_read_length": 10,
        "si_read_length": null,
        "read_type_to_bcl2fastq_filename": {
            "I1": "I1",
            "I2": null,
            "R1": "R1",
            "R2": "R2"
        },
        "rna_read2_length": null,
        "rna_read2_offset": 0,
        "read_type_to_bcl_processor_filename": {
            "I1": "I1",
            "I2": null,
            "R1": "RA",
            "R2": null
        }
    },
    barcode_whitelist = "737K-august-2016",
    is_antibody_only = false,
    barcodes_detected = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u8c0aa715b4/files/barcodes_detected.csv",
    gem_groups = [
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1
    ],
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
)