@include "rna/_sc_multi_defs.mro"

call SAMPLE_REPORTER(
    sample_outs               = {
        all_genes_matrix_h5:  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix.h5",
        all_genes_matrix_mex: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix",
        bam_file:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_dimitri-multi.bam",
        bam_index_file:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_dimitri-multi.bam.bai",
        feature_reference:    null,
        filtered_barcodes:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_barcodes.csv",
        matrix_h5:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix.h5",
        matrix_mex:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix",
        metrics_summary:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_summary.json",
        molecule_info:        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/molecule_info_dimitri-multi.h5",
        per_barcode_metrics:  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_per_barcode_metrics.csv",
        sample:               "dimitri-multi",
        target_panel:         null,
    },
    sample_id                 = "dimitri-multi",
    sample_desc               = "",
    config                    = {
        disable_count:       false,
        disable_multi:       false,
        disable_multi_count: false,
        disable_vdj_b:       false,
        disable_vdj_t:       false,
        has_no_vdj_ref:      false,
    },
    count_pipestance_type     = "SC_RNA_COUNTER_CS",
    count_analyzer            = {
        analysis:         "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/analysis",
        analysis_csv:     "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/analysis_csv",
        cloupe_matrix_h5: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork_dimitri-multi/join-ucc6a7a7d7a/files/cloupe_matrix_h5.h5",
        summary:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/summary.json",
    },
    crispr_analyzer           = null,
    targeted_analyzer         = null,
    reference_path            = "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
    barcode_summary           = "/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/WRITE_BARCODE_SUMMARY/fork0/chnk0-ucc6a7a7c4d/files/barcode_summary.h5",
    cell_calling_config       = {
        cell_barcodes:                  null,
        disable_ab_aggregate_detection: false,
        force_cells:                    null,
        override_library_types:         null,
        override_mode:                  null,
        recovered_cells:                null,
    },
    sample_assignment_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/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS/fork0/chnk0-ucc6a7a7cde/files/dimitri-multi_summary.json",
    target_features_metrics   = null,
    cells_per_tag             = null,
    is_antibody_only          = false,
)
