@include "rna/_cr_lib_stages.mro"

call BUILD_VDJ_WS_CONTENTS as BUILD_VDJ_T_WS_CONTENTS(
    metrics_summary    = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce0/files/metrics_summary_json.json",
    receptor           = "TR",
    vdj_inputs         = {
        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_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",
    },
    sequencing_metrics = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/sequencing_metrics.smf.json",
    vdj_ws_json        = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce0/files/web_summary_data.json",
)
