@include "rna/_sc_multi_defs.mro"

call SPLIT_VDJ_INPUTS(
    vdj_inputs          = [
        {
            chain_type:                  "IG",
            chemistry:                   "SCVDJ_auto",
            custom_chemistry_def:        null,
            denovo:                      false,
            force_cells:                 null,
            ground_truth_clonotype_path: null,
            initial_reads:               null,
            inner_enrichment_primers:    null,
            physical_library_id:         "VDJB_1",
            primer_initial_reads:        null,
            primers: [
                {
                    "name": "P5",
                    "seq": "AATGATACGGCGACCACCGAGATCT",
                },
                {
                    "name": "P7",
                    "seq": "CAAGCAGAAGACGGCATACGAGAT",
                },
                {
                    "name": "R1",
                    "seq": "ACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                },
                {
                    "name": "R2",
                    "seq": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT",
                },
                {
                    "name": "polyA",
                    "seq": "AAAAAAAAAAAAAAAAAAAA",
                },
                {
                    "name": "rt_primer",
                    "seq": "AAGCAGTGGTATCAACGCAGAGTACAT",
                },
                {
                    "name": "spacer",
                    "seq": "TTTCTTATATGGG",
                },
            ],
            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,
                },
            ],
            special_genomic_regions:     null,
            subsample_rate:              null,
        },
        {
            chain_type:                  "TR",
            chemistry:                   "SCVDJ_auto",
            custom_chemistry_def:        null,
            denovo:                      false,
            force_cells:                 null,
            ground_truth_clonotype_path: null,
            initial_reads:               null,
            inner_enrichment_primers:    null,
            physical_library_id:         "VDJT_1",
            primer_initial_reads:        null,
            primers: [
                {
                    "name": "P5",
                    "seq": "AATGATACGGCGACCACCGAGATCT",
                },
                {
                    "name": "P7",
                    "seq": "CAAGCAGAAGACGGCATACGAGAT",
                },
                {
                    "name": "R1",
                    "seq": "ACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                },
                {
                    "name": "R2",
                    "seq": "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT",
                },
                {
                    "name": "polyA",
                    "seq": "AAAAAAAAAAAAAAAAAAAA",
                },
                {
                    "name": "rt_primer",
                    "seq": "AAGCAGTGGTATCAACGCAGAGTACAT",
                },
                {
                    "name": "spacer",
                    "seq": "TTTCTTATATGGG",
                },
            ],
            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,
                },
            ],
            special_genomic_regions:     null,
            subsample_rate:              null,
        },
    ],
    vdj_chemistry_types = [
        "SCVDJ-R2",
        "SCVDJ-R2",
    ],
    vdj_receptors       = [
        "IG",
        "TR",
    ],
)
