@include "rna/_sc_multi_defs.mro"

map call _GEM_WELL_CHEMISTRY_DETECTOR(
    gem_well_inputs     = split [
        {
            common_inputs: {
                multi_config_sha: "441f739f093e36c43f57328492fe5aa9703c212f8c5a330ff0ef60c31a5f08c4",
                sample_desc:      "",
                sample_id:        "dimitri-multi",
            },
            count_inputs: {
                chemistry:                   "auto",
                custom_chemistry_def:        null,
                enforce_library_concordance: true,
                feature_reference:           null,
                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,
                    },
                ],
            },
            vdj_inputs: [
                {
                    chain_type:           "IG",
                    chemistry:            "SCVDJ_auto",
                    custom_chemistry_def: 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,
                        },
                    ],
                },
                {
                    chain_type:           "TR",
                    chemistry:            "SCVDJ_auto",
                    custom_chemistry_def: 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,
                        },
                    ],
                },
            ],
        },
    ],
    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",
    },
    basic_config        = {
        disable_count:       false,
        disable_multi:       false,
        disable_multi_count: false,
        disable_vdj:         false,
    },
    count_allowed_chems = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3P_auto",
        "SC5P_auto",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3",
        "SC3Pv3LT",
        "SC3Pv3HT",
        "SC5P-PE",
        "SC5P-R1",
        "SC5P-R2",
        "SC5PHT",
        "SC-FB",
        "ARC-v1",
    ],
)
