@include "rna/_sc_multi_defs.mro"

call COUNT_GEM_WELL_PROCESSOR(
    gem_group              = 1,
    sample_id              = "count-PAXUGA_Relapse",
    multi_config_sha       = null,
    inputs                 = {
        aligner:                     null,
        cell_calling_config: {
            cell_barcodes:                  null,
            disable_ab_aggregate_detection: false,
            force_cells:                    null,
            override_library_types:         null,
            override_mode:                  null,
            recovered_cells:                null,
        },
        custom_chemistry_def:        null,
        enforce_library_concordance: true,
        feature_reference:           null,
        force_sample_barcodes:       null,
        gene_index:                  "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-uac0168879c/files/gene_index.json",
        include_introns:             false,
        initial_reads:               null,
        no_bam:                      false,
        no_target_umi_filter:        false,
        primers: [
            {
                "name": "P5",
                "seq": "AATGATACGGCGACCACCGAGATCT",
            },
            {
                "name": "P7",
                "seq": "CAAGCAGAAGACGGCATACGAGAT",
            },
            {
                "name": "R1",
                "seq": "ACACTCTTTCCCTACACGACG",
            },
            {
                "name": "R2",
                "seq": "GTGACTGGAGTTCAGACGTGTG",
            },
            {
                "name": "switch_oligo",
                "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG",
            },
            {
                "name": "polyA",
                "seq": "AAAAAAAAAAAAAAAAAAAA",
            },
        ],
        r1_length:                   null,
        r2_length:                   null,
        reference_path:              "/gpfs/data/sequence/cellranger-refdata/refdata-gex-GRCh38-2020-A",
        sample_def: [
            {
                "fastq_id": null,
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": null,
                "lanes": null,
                "library_type": "Gene Expression",
                "read_path": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/fastq",
                "sample_indices": ["any"],
                "sample_names": ["PAXUGA_Relapse"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
        subsample_rate:              null,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
    chem                   = {
        chemistry_type:   "SC3Pv3",
        is_antibody_only: false,
    },
    libraries_to_translate = [],
    is_pd                  = false,
    disable_multi          = true,
    multi_graph            = null,
)
