@include "rna/_sc_vdj_contig_assembler.mro"

call SC_VDJ_CONTIG_ASSEMBLER(
    gem_well              = 1,
    chemistry_def         = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: "737K-august-2016",
            },
        ],
        description:  "Single Cell V(D)J R2-only",
        endedness:    "five_prime",
        name:         "SCVDJ-R2",
        rna: {
            length:     null,
            min_length: null,
            offset:     0,
            read_type:  "R2",
        },
        rna2:         null,
        strandedness: "-",
        umi: {
            length:     10,
            min_length: null,
            offset:     16,
            read_type:  "R1",
        },
    },
    chunks                = [
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": "737K-august-2016",
                    },
                ],
                "description": "Single Cell V(D)J R2-only",
                "endedness": "five_prime",
                "name": "SCVDJ-R2",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "-",
                "umi": {
                    "length": 10,
                    "min_length": null,
                    "offset": 16,
                    "read_type": "R1",
                },
            },
            "chunk_id": 0,
            "fastq_id": "dimitri_TCR",
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "VDJ",
            "read_group": "dimitri-multi:0:1:HKLTCBGXL:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    r1_length             = null,
    r2_length             = null,
    initial_reads         = null,
    subsample_rate        = null,
    vdj_reference_folder  = "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
    denovo                = false,
    force_cells           = null,
    inner_primers         = null,
    receptor              = "TR",
    gex_filtered_barcodes = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_barcodes.csv",
    is_antibody_only      = false,
    is_non_targeted_gex   = true,
)
