@include "rna/sc_multi_core.mro"

call SC_MULTI_CORE(
    common_input          = {
        multi_config_sha: null,
        sample_desc:      "",
        sample_id:        "count-PAXUGA_Relapse",
    },
    count_input           = {
        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,
        },
        chemistry:                       "auto",
        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",
        genetic_demux_params:            null,
        include_introns:                 false,
        initial_reads:                   null,
        no_bam:                          false,
        no_secondary_analysis:           false,
        no_target_umi_filter:            false,
        primer_initial_reads:            null,
        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",
            },
        ],
        probe_barcodes_intended_pairing: null,
        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,
            },
        ],
        special_genomic_regions:         null,
        subsample_rate:                  null,
        tenx_cmos:                       null,
        throughput:                      null,
        trim_polya_min_score:            20,
        trim_tso_min_score:              20,
    },
    vdj_inputs            = [],
    vdj_gen_inputs        = null,
    basic_config          = {
        disable_count:       false,
        disable_multi:       true,
        disable_multi_count: true,
        disable_vdj:         true,
    },
    multi_config          = null,
    multi_graph           = null,
    is_pd                 = false,
    count_allowed_chems   = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3P_auto",
        "SC5P_auto",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3",
        "SC3Pv3LT",
        "SC5P-PE",
        "SC5P-R1",
        "SC5P-R2",
        "SC-FB",
        "ARC-v1",
    ],
    count_pipestance_type = "SC_RNA_COUNTER_CS",
)
