@include "rna/_sc_multi_defs.mro"

call MULTI_GEM_WELL_PROCESSOR(
    gem_group              = 1,
    sample_id              = "dimitri-multi",
    multi_config_sha       = "441f739f093e36c43f57328492fe5aa9703c212f8c5a330ff0ef60c31a5f08c4",
    config                 = {
        disable_count:       false,
        disable_multi:       false,
        disable_multi_count: false,
        disable_vdj_b:       false,
        disable_vdj_t:       false,
        has_no_vdj_ref:      false,
    },
    is_pd                  = false,
    count_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:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-ucc6a7a71a3/files/gene_index.json",
        include_introns:             false,
        initial_reads:               null,
        min_assignment_confidence:   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:              "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
        sample_def: [
            {
                fastq_id:        "dimitri_RNA",
                fastq_mode:      "ILMN_BCL2FASTQ",
                gem_group:       1,
                lanes:           null,
                library_type:    "Gene Expression",
                read_path:       "/scratch/etanis/ST-118/FASTQ/",
                sample_indices:  null,
                sample_names:    ["dimitri_RNA"],
                subsample_rate:  null,
                target_set:      null,
                target_set_name: null,
            },
        ],
        subsample_rate:              null,
        targeting_method:            null,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
    count_chem             = {
        chemistry_type:   "SC5P-R2",
        is_antibody_only: false,
    },
    libraries_to_translate = [],
    multi_graph            = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-ucc6a7a7197/files/multi_graph.json",
    vdj_t_inputs           = {
        custom_chemistry_def:     null,
        denovo:                   false,
        force_cells:              null,
        initial_reads:            null,
        inner_enrichment_primers: null,
        r1_length:                null,
        r2_length:                null,
        sample_def: [
            {
                "fastq_id": "dimitri_TCR",
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": 1,
                "lanes": null,
                "library_type": "VDJ",
                "read_path": "/scratch/etanis/ST-118/FASTQ/",
                "sample_indices": null,
                "sample_names": ["dimitri_TCR"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
        subsample_rate:           null,
    },
    vdj_t_chem_type        = "SCVDJ-R2",
    vdj_t_receptor         = "TR",
    vdj_b_inputs           = {
        custom_chemistry_def:     null,
        denovo:                   false,
        force_cells:              null,
        initial_reads:            null,
        inner_enrichment_primers: null,
        r1_length:                null,
        r2_length:                null,
        sample_def: [
            {
                "fastq_id": "dimitri_BCR",
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": 1,
                "lanes": null,
                "library_type": "VDJ",
                "read_path": "/scratch/etanis/ST-118/FASTQ/",
                "sample_indices": null,
                "sample_names": ["dimitri_BCR"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
        subsample_rate:           null,
    },
    vdj_b_chem_type        = "SCVDJ-R2",
    vdj_b_receptor         = "IG",
    vdj_gen_inputs         = {
        reference_path:     "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
        vdj_reference_path: "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
    },
)
