@include "rna/_sc_multi_defs.mro"

call STRUCTIFY_PER_SAMPLE_OUTS(
    sample_bams           = [
        {
            bam_file:       "/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/MULTI_WRITE_PER_SAMPLE_BAM/fork0/join-ucc6a7a7cde/files/pos_sorted_dimitri-multi.bam",
            bam_index_file: "/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/MULTI_WRITE_PER_SAMPLE_BAM/fork0/join-ucc6a7a7cde/files/pos_sorted_dimitri-multi.bam.bai",
            sample:         "dimitri-multi",
        },
        {
            bam_file:       "/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/MULTI_WRITE_PER_SAMPLE_BAM/fork0/join-ucc6a7a7cde/files/pos_sorted_unassigned.bam",
            bam_index_file: "/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/MULTI_WRITE_PER_SAMPLE_BAM/fork0/join-ucc6a7a7cde/files/pos_sorted_unassigned.bam.bai",
            sample:         "unassigned",
        },
    ],
    sample_metrics        = [
        {
            per_barcode_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/MULTI_COLLATE_PER_SAMPLE_METRICS/fork0/chnk0-ucc6a7a7cde/files/per_barcode_metrics.csv",
            per_lib_type_metrics: {},
            sample:               "dimitri-multi",
            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/MULTI_COLLATE_PER_SAMPLE_METRICS/fork0/chnk0-ucc6a7a7cde/files/summary.json",
        },
    ],
    sample_molecule_infos = [
        {
            h5_file: "/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/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO/fork0/chnk0-ucc6a7a7ce2/files/molecule_info_dimitri-multi.h5",
            sample:  "dimitri-multi",
            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/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO/fork0/chnk0-ucc6a7a7ce2/files/dimitri-multi_summary.json",
        },
    ],
    sample_matrices       = [
        {
            all_genes_matrix_h5:  "/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/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/chnk0-ucc6a7a7cdf/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/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/chnk0-ucc6a7a7cdf/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix",
            filtered_barcodes:    "/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/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/chnk0-ucc6a7a7cdf/files/dimitri-multi_filtered_barcodes.csv",
            matrix_h5:            "/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/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/chnk0-ucc6a7a7cdf/files/dimitri-multi_filtered_feature_barcode_matrix.h5",
            matrix_mex:           "/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/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/chnk0-ucc6a7a7cdf/files/dimitri-multi_filtered_feature_barcode_matrix",
            sample:               "dimitri-multi",
        },
    ],
    multi_graph           = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-ucc6a7a7197/files/multi_graph.json",
    feature_reference     = null,
    target_panel          = null,
)
