@include "_basic_sc_rna_counter_stages.mro"

call COUNT_GENES(
    sample_id = "Nash1",
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-ud74eb27f4a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-ud74eb27f4a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-ud74eb27f4d/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/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-ud74eb27825/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
    ],
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
)