@include "rna/sc_multi_core.mro"

call MULTI_WEBSUMMARY_BUILDER(
    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",
    },
    vdj_t_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",
    vdj_t_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",
    vdj_t_receptor               = "TR",
    vdj_t_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_t_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",
    disable_vdj_t                = false,
    vdj_b_metrics_summary        = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce4/files/metrics_summary_json.json",
    vdj_b_ws_json                = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce4/files/web_summary_data.json",
    vdj_b_receptor               = "IG",
    vdj_b_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,
    },
    disable_vdj_b                = false,
    vdj_b_sequencing_metrics     = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/sequencing_metrics.smf.json",
    per_sample_metrics           = {
        "dimitri-multi": "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0/chnk0-ucc6a7a7db5/files/dimitri-multi_summary.json",
    },
    library_metrics              = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ucc6a7a7d79/files/metrics_summary_json.json",
    sequencing_metrics           = "/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/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/sequencing_metrics.smf.json",
    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",
    common_inputs                = {
        multi_config_sha: "441f739f093e36c43f57328492fe5aa9703c212f8c5a330ff0ef60c31a5f08c4",
        sample_desc:      "",
        sample_id:        "dimitri-multi",
    },
    count_inputs                 = {
        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,
    },
    tag_contaminant_info         = null,
    sample_tsne_plots            = {
        "dimitri-multi": "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0/chnk0-ucc6a7a7db5/files/dimitri-multi_sample_tsne_plots.json",
    },
    barcode_rank_plots           = {
        "Gene Expression": "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0/chnk0-ucc6a7a7db5/files/Gene Expression_Gene Expression_barcode_rank_plot.json",
    },
    antibody_histograms          = null,
    jibes_biplot_histogram       = null,
    cmo_tsne_plot                = null,
    target_set_name              = null,
    targeted_per_feature_metrics = null,
)
