@include "rna/sc_multi_core.mro"

call SC_MULTI_CORE(
    common_input          = {
        multi_config_sha: "441f739f093e36c43f57328492fe5aa9703c212f8c5a330ff0ef60c31a5f08c4",
        sample_desc:      "",
        sample_id:        "dimitri-multi",
    },
    count_input           = {
        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,
        },
        chemistry:                       "auto",
        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",
        genetic_demux_params:            null,
        include_introns:                 false,
        initial_reads:                   null,
        min_assignment_confidence:       null,
        no_bam:                          false,
        no_secondary_analysis:           false,
        no_target_umi_filter:            false,
        primer_initial_reads:            null,
        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",
            },
        ],
        probe_barcodes_intended_pairing: 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,
            },
        ],
        special_genomic_regions:         null,
        subsample_rate:                  null,
        targeting_method:                null,
        tenx_cmos:                       null,
        throughput:                      null,
        trim_polya_min_score:            20,
        trim_tso_min_score:              20,
    },
    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_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,
    },
    multi_config          = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-ucc6a7a7197/files/config.csv",
    multi_graph           = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-ucc6a7a7197/files/multi_graph.json",
    is_pd                 = 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",
    ],
    count_pipestance_type = "SC_RNA_COUNTER_CS",
)
