@include "rna/sc_multi_core.mro"

call BUILD_VDJ_OUTPUTS_CS(
    multi_core = {
        count_analyzer: {
            antibody_analyzer: null,
            crispr_analyzer:   null,
            rna_analyzer:      null,
            targeted_analyzer: null,
        },
        detect_count_chem: {
            chemistry_type:   "SC5P-R2",
            is_antibody_only: false,
        },
        disable_feat: {
            disable_antibody:       true,
            disable_crispr:         true,
            disable_legacy_stages:  true,
            disable_library_cloupe: true,
            disable_multiplexing:   true,
            disable_targeted:       true,
        },
        full_config: {
            disable_count:       false,
            disable_multi:       false,
            disable_multi_count: false,
            disable_vdj_b:       false,
            disable_vdj_t:       false,
            has_no_vdj_ref:      false,
        },
        multi_gw: {
            count: {
                basic_counter_outs: {
                    aggregate_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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/aggregate_barcodes.csv",
                    alignments: [
                        "/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/ALIGN_AND_COUNT/fork0/chnk00-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk01-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk02-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk03-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk04-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk05-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk06-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk07-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk08-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk09-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk10-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk11-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk12-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk13-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk14-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk15-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk16-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk17-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk18-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk19-ucc6a7a77c8/files/pos_sorted.asf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk20-ucc6a7a77c8/files/pos_sorted.asf",
                    ],
                    annotation_files:              null,
                    assign_tags: {
                        assignment_confidence_table:   null,
                        cells_per_tag:                 null,
                        gem_well_inferred_throughputs: null,
                        gem_well_throughput:           null,
                        jibes_model_summary:           null,
                        jibes_parameters:              null,
                        jibes_summary_data:            null,
                        marginal_tag_frequencies:      null,
                        non_tag_assignments:           "/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/CALL_TAGS_JIBES/fork0/join-ucc6a7a7cdb/files/non_tag_assignments.json",
                        sample_assignment_metrics: {
                            dimitri-multi: "/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",
                        },
                        sample_barcodes_json:          "/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/sample_barcodes.json",
                        tag_assigner_pickle:           null,
                        tag_call_metrics_json:         "/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/MERGE_METRICS/fork0/chnk0-ucc6a7a7ce0/files/summary.json",
                        tag_calls_per_cell:            null,
                        tag_calls_summary:             null,
                        tag_contaminant_info:          null,
                        tag_umi_thresholds_csv:        null,
                        tag_umi_thresholds_json:       null,
                    },
                    bam_header:                    "/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/ALIGN_AND_COUNT/fork0/join-ucc6a7a77c8/files/bam_header",
                    barcode_correction_csv:        "/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/ALIGN_AND_COUNT/fork0/join-ucc6a7a77c8/files/barcode_summary.csv",
                    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",
                    barcode_whitelist:             "737K-august-2016",
                    bc_umi_info: [
                        "/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/ALIGN_AND_COUNT/fork0/chnk00-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk01-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk02-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk03-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk04-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk05-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk06-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk07-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk08-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk09-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk10-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk11-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk12-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk13-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk14-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk15-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk16-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk17-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk18-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk19-ucc6a7a77c8/files/bc_umi_info.bui",
                        "/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/ALIGN_AND_COUNT/fork0/chnk20-ucc6a7a77c8/files/bc_umi_info.bui",
                    ],
                    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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_barcodes.csv",
                    filtered_gene_bc_matrices_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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_matrices_h5.h5",
                    filtered_gene_bc_matrices_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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_matrices_mex",
                    gem_groups:                    [1],
                    gem_well_alignment_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/COLLATE_METRICS/fork0/chnk0-ucc6a7a7c4d/files/summary.json",
                    merged_subsampling_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/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ucc6a7a7cd4/files/merged_metrics.pickle",
                    molecule_info:                 "/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/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ucc6a7a7ccd/files/molecule_info_non_multiplexed.h5",
                    multi_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_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",
                        },
                    ],
                    multi_molecule_info: [
                        {
                            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",
                        },
                    ],
                    multi_pos_sorted_bam: [
                        {
                            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",
                        },
                    ],
                    nonambient_cell_calls:         "/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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/nonambient_calls.csv",
                    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/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ucc6a7a7c4d/files/per_barcode_metrics.csv",
                    per_barcode_metrics_shard: [
                        "/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/ALIGN_AND_COUNT/fork0/chnk00-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk01-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk02-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk03-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk04-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk05-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk06-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk07-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk08-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk09-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk10-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk11-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk12-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk13-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk14-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk15-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk16-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk17-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk18-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk19-ucc6a7a77c8/files/metrics_shard.bmsf",
                        "/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/ALIGN_AND_COUNT/fork0/chnk20-ucc6a7a77c8/files/metrics_shard.bmsf",
                    ],
                    possorted_genome_bam:          null,
                    possorted_genome_bam_index:    null,
                    raw_gene_bc_matrices_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/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ucc6a7a7c4d/files/raw_feature_bc_matrix.h5",
                    raw_gene_bc_matrices_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/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0-ucc6a7a7c4d/files/raw_feature_bc_matrix",
                    read_chunks: [
                        {
                            chemistry: {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-august-2016",
                                    },
                                ],
                                "description": "Single Cell 5' R2-only",
                                "endedness": "five_prime",
                                "name": "SC5P-R2",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2",
                                },
                                "rna2": null,
                                "strandedness": "-",
                                "umi": {
                                    "length": 10,
                                    "min_length": null,
                                    "offset": 16,
                                    "read_type": "R1",
                                },
                            },
                            chunk_id:       0,
                            fastq_id:       "dimitri_RNA",
                            fastqs: {
                                "i1": null,
                                "i2": null,
                                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R1_001.fastq.gz",
                                "r1_interleaved": false,
                                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R2_001.fastq.gz",
                            },
                            gem_group:      1,
                            library_id:     0,
                            library_type:   "Gene Expression",
                            read_group:     "dimitri-multi:0:1:HKLTCBGXL:1",
                            read_lengths:   {},
                            subsample_rate: null,
                        },
                    ],
                    read_shards: {
                        corrected_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk00-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk01-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk02-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk03-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk04-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk05-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk06-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk07-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk08-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk09-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk10-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk11-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk12-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk13-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk14-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk15-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk16-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk17-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk18-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk19-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk20-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk21-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk22-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk23-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk24-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk25-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk26-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk27-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk28-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk29-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk30-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk31-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk32-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk33-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk34-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk35-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk36-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk37-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk38-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk39-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk40-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk41-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk42-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk43-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk44-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk45-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk46-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk47-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk48-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk49-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk50-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk51-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk52-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk53-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk54-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk55-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk56-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk57-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk58-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk59-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk60-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk61-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk62-ucc6a7a77b3/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk63-ucc6a7a77b3/files/valid_shard.shard",
                        ],
                        invalid_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk00-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk01-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk02-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk03-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk04-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk05-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk06-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk07-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk08-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk09-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk10-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk11-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk12-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk13-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk14-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk15-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk16-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk17-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk18-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk19-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk20-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk21-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk22-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk23-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk24-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk25-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk26-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk27-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk28-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk29-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk30-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk31-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk32-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk33-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk34-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk35-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk36-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk37-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk38-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk39-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk40-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk41-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk42-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk43-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk44-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk45-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk46-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk47-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk48-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk49-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk50-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk51-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk52-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk53-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk54-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk55-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk56-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk57-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk58-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk59-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk60-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk61-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk62-ucc6a7a77b3/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk63-ucc6a7a77b3/files/invalid_shard.shard",
                        ],
                        valid_reads: ["/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/chnk0-ucc6a7a71c6/files/valid.shard"],
                    },
                    sample_assignment_metrics: {
                        dimitri-multi: "/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",
                    },
                    sample_barcodes_json:          "/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/sample_barcodes.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",
                    slfe_feature_reference:        "/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/split-ucc6a7a71c0/files/feature_reference.frf.bincode",
                    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/MERGE_METRICS/fork0/chnk0-ucc6a7a7d61/files/summary.json",
                    target_set_name:               null,
                },
                setup_chunks_outs: {
                    barcode_whitelist: "737K-august-2016",
                    chemistry_def: {
                        barcode: [
                            {
                                "kind": "gel_bead",
                                "length": 16,
                                "offset": 0,
                                "read_type": "R1",
                                "whitelist": "737K-august-2016",
                            },
                        ],
                        description:  "Single Cell 5' R2-only",
                        endedness:    "five_prime",
                        name:         "SC5P-R2",
                        rna: {
                            "length": null,
                            "min_length": null,
                            "offset": 0,
                            "read_type": "R2",
                        },
                        rna2:         null,
                        strandedness: "-",
                        umi: {
                            "length": 10,
                            "min_length": null,
                            "offset": 16,
                            "read_type": "R1",
                        },
                    },
                    chunks: [
                        {
                            chemistry: {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-august-2016",
                                    },
                                ],
                                "description": "Single Cell 5' R2-only",
                                "endedness": "five_prime",
                                "name": "SC5P-R2",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2",
                                },
                                "rna2": null,
                                "strandedness": "-",
                                "umi": {
                                    "length": 10,
                                    "min_length": null,
                                    "offset": 16,
                                    "read_type": "R1",
                                },
                            },
                            chunk_id:       0,
                            fastq_id:       "dimitri_RNA",
                            fastqs: {
                                "i1": null,
                                "i2": null,
                                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R1_001.fastq.gz",
                                "r1_interleaved": false,
                                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_RNA_S1_L001_R2_001.fastq.gz",
                            },
                            gem_group:      1,
                            library_id:     0,
                            library_type:   "Gene Expression",
                            read_group:     "dimitri-multi:0:1:HKLTCBGXL:1",
                            read_lengths:   {},
                            subsample_rate: null,
                        },
                    ],
                },
                target_outs: {
                    bait_fasta:                null,
                    disable_target_umi_filter: true,
                    disable_targeted:          true,
                    probe_set:                 null,
                    rps_limit:                 null,
                    summary:                   null,
                    target_gene_indices:       null,
                    target_panel:              null,
                    target_panel_or_probe_set: null,
                    target_set_name:           null,
                    targeting_method:          null,
                },
            },
            vdj_b: {
                assembler_outs: {
                    assemblable_reads_per_bc: "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/assemblable_reads_per_bc.arp.bincode",
                    barcode_support:          "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/barcode_support.csv",
                    barcodes_in_chunks: [
                        "/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/ASSEMBLE_VDJ/fork0/chnk000-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk001-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk002-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk003-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk004-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk005-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk006-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk007-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk008-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk009-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk010-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk011-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk012-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk013-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk014-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk015-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk016-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk017-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk018-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk019-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk020-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk021-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk022-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk023-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk024-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk025-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk026-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk027-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk028-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk029-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk030-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk031-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk032-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk033-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk034-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk035-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk036-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk037-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk038-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk039-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk040-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk041-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk042-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk043-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk044-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk045-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk046-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk047-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk048-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk049-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk050-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk051-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk052-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk053-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk054-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk055-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk056-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk057-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk058-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk059-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk060-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk061-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk062-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk063-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk064-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk065-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk066-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk067-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk068-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk069-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk070-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk071-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk072-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk073-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk074-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk075-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk076-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk077-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk078-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk079-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk080-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk081-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk082-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk083-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk084-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk085-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk086-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk087-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk088-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk089-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk090-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk091-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk092-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk093-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk094-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk095-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk096-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk097-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk098-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk099-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk100-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk101-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk102-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk103-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk104-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk105-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk106-ucc6a7a72ce/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk107-ucc6a7a72ce/files/barcodes_in_chunk.json",
                    ],
                    contig_annotations:       "/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/HANDLE_GEX_CELLS/fork0/chnk0-ucc6a7a7ccd/files/contig_annotations.json",
                    contig_bam:               "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/contig_bam.bam",
                    contig_bam_bai:           "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/contig_bam.bam.bai",
                    corrected_barcode_counts: "/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/RUST_BRIDGE/fork0/join-ucc6a7a72b0/files/corrected_barcode_counts.json",
                    gem_groups: [
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                    ],
                    n50_n50_rpu:              288,
                    processed_read_pairs:     20716612,
                    raw_barcode_counts:       "/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/RUST_BRIDGE/fork0/join-ucc6a7a72b0/files/raw_barcode_counts.json",
                    read_shards: {
                        corrected_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk0-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk1-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk2-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk3-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk4-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk5-ucc6a7a72ab/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk6-ucc6a7a72ab/files/valid_shard.shard",
                        ],
                        invalid_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk0-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk1-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk2-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk3-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk4-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk5-ucc6a7a72ab/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk6-ucc6a7a72ab/files/invalid_shard.shard",
                        ],
                        valid_reads: ["/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/chnk0-ucc6a7a71c0/files/valid.shard"],
                    },
                    report:                   "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/report.txt",
                    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",
                    summary:                  "/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/MERGE_METRICS/fork0/chnk0-ucc6a7a73e1/files/summary.json",
                    summary_tsv:              "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/summary_tsv.tsv",
                    total_read_pairs:         56633794,
                    umi_summary_tsv:          "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/umi_summary_tsv.tsv",
                    unmapped_sample_fastq:    "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/unmapped_sample_fastq.fastq",
                },
                setup_chunks_outs: {
                    barcode_whitelist: "737K-august-2016",
                    chemistry_def: {
                        barcode: [
                            {
                                "kind": "gel_bead",
                                "length": 16,
                                "offset": 0,
                                "read_type": "R1",
                                "whitelist": "737K-august-2016",
                            },
                        ],
                        description:  "Single Cell V(D)J R2-only",
                        endedness:    "five_prime",
                        name:         "SCVDJ-R2",
                        rna: {
                            "length": null,
                            "min_length": null,
                            "offset": 0,
                            "read_type": "R2",
                        },
                        rna2:         null,
                        strandedness: "-",
                        umi: {
                            "length": 10,
                            "min_length": null,
                            "offset": 16,
                            "read_type": "R1",
                        },
                    },
                    chunks: [
                        {
                            chemistry: {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-august-2016",
                                    },
                                ],
                                "description": "Single Cell V(D)J R2-only",
                                "endedness": "five_prime",
                                "name": "SCVDJ-R2",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2",
                                },
                                "rna2": null,
                                "strandedness": "-",
                                "umi": {
                                    "length": 10,
                                    "min_length": null,
                                    "offset": 16,
                                    "read_type": "R1",
                                },
                            },
                            chunk_id:       0,
                            fastq_id:       "dimitri_BCR",
                            fastqs: {
                                "i1": null,
                                "i2": null,
                                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_BCR_S1_L001_R1_001.fastq.gz",
                                "r1_interleaved": false,
                                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_BCR_S1_L001_R2_001.fastq.gz",
                            },
                            gem_group:      1,
                            library_id:     0,
                            library_type:   "VDJ",
                            read_group:     "dimitri-multi:0:1:HKLTCBGXL:1",
                            read_lengths:   {},
                            subsample_rate: null,
                        },
                    ],
                },
            },
            vdj_t: {
                assembler_outs: {
                    assemblable_reads_per_bc: "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/assemblable_reads_per_bc.arp.bincode",
                    barcode_support:          "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/barcode_support.csv",
                    barcodes_in_chunks: [
                        "/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/ASSEMBLE_VDJ/fork0/chnk00-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk01-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk02-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk03-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk04-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk05-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk06-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk07-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk08-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk09-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk10-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk11-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk12-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk13-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk14-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk15-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk16-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk17-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk18-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk19-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk20-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk21-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk22-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk23-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk24-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk25-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk26-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk27-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk28-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk29-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk30-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk31-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk32-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk33-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk34-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk35-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk36-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk37-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk38-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk39-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk40-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk41-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk42-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk43-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk44-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk45-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk46-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk47-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk48-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk49-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk50-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk51-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk52-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk53-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk54-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk55-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk56-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk57-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk58-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk59-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk60-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk61-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk62-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk63-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk64-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk65-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk66-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk67-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk68-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk69-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk70-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk71-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk72-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk73-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk74-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk75-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk76-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk77-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk78-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk79-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk80-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk81-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk82-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk83-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk84-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk85-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk86-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk87-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk88-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk89-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk90-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk91-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk92-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk93-ucc6a7a72e6/files/barcodes_in_chunk.json",
                        "/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/ASSEMBLE_VDJ/fork0/chnk94-ucc6a7a72e6/files/barcodes_in_chunk.json",
                    ],
                    contig_annotations:       "/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/HANDLE_GEX_CELLS/fork0/chnk0-ucc6a7a7ccd/files/contig_annotations.json",
                    contig_bam:               "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/contig_bam.bam",
                    contig_bam_bai:           "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/contig_bam.bam.bai",
                    corrected_barcode_counts: "/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/RUST_BRIDGE/fork0/join-ucc6a7a72c2/files/corrected_barcode_counts.json",
                    gem_groups: [
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                    ],
                    n50_n50_rpu:              2159,
                    processed_read_pairs:     46574590,
                    raw_barcode_counts:       "/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/RUST_BRIDGE/fork0/join-ucc6a7a72c2/files/raw_barcode_counts.json",
                    read_shards: {
                        corrected_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk00-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk01-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk02-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk03-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk04-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk05-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk06-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk07-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk08-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk09-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk10-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk11-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk12-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk13-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk14-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk15-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk16-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk17-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk18-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk19-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk20-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk21-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk22-ucc6a7a72b9/files/valid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk23-ucc6a7a72b9/files/valid_shard.shard",
                        ],
                        invalid_reads: [
                            "/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/BARCODE_CORRECTION/fork0/chnk00-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk01-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk02-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk03-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk04-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk05-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk06-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk07-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk08-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk09-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk10-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk11-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk12-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk13-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk14-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk15-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk16-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk17-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk18-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk19-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk20-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk21-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk22-ucc6a7a72b9/files/invalid_shard.shard",
                            "/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/BARCODE_CORRECTION/fork0/chnk23-ucc6a7a72b9/files/invalid_shard.shard",
                        ],
                        valid_reads: ["/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/chnk0-ucc6a7a71c0/files/valid.shard"],
                    },
                    report:                   "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/report.txt",
                    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",
                    summary:                  "/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/MERGE_METRICS/fork0/chnk0-ucc6a7a7409/files/summary.json",
                    summary_tsv:              "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/summary_tsv.tsv",
                    total_read_pairs:         58185432,
                    umi_summary_tsv:          "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/umi_summary_tsv.tsv",
                    unmapped_sample_fastq:    "/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/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/unmapped_sample_fastq.fastq",
                },
                setup_chunks_outs: {
                    barcode_whitelist: "737K-august-2016",
                    chemistry_def: {
                        barcode: [
                            {
                                "kind": "gel_bead",
                                "length": 16,
                                "offset": 0,
                                "read_type": "R1",
                                "whitelist": "737K-august-2016",
                            },
                        ],
                        description:  "Single Cell V(D)J R2-only",
                        endedness:    "five_prime",
                        name:         "SCVDJ-R2",
                        rna: {
                            "length": null,
                            "min_length": null,
                            "offset": 0,
                            "read_type": "R2",
                        },
                        rna2:         null,
                        strandedness: "-",
                        umi: {
                            "length": 10,
                            "min_length": null,
                            "offset": 16,
                            "read_type": "R1",
                        },
                    },
                    chunks: [
                        {
                            chemistry: {
                                "barcode": [
                                    {
                                        "kind": "gel_bead",
                                        "length": 16,
                                        "offset": 0,
                                        "read_type": "R1",
                                        "whitelist": "737K-august-2016",
                                    },
                                ],
                                "description": "Single Cell V(D)J R2-only",
                                "endedness": "five_prime",
                                "name": "SCVDJ-R2",
                                "rna": {
                                    "length": null,
                                    "min_length": null,
                                    "offset": 0,
                                    "read_type": "R2",
                                },
                                "rna2": null,
                                "strandedness": "-",
                                "umi": {
                                    "length": 10,
                                    "min_length": null,
                                    "offset": 16,
                                    "read_type": "R1",
                                },
                            },
                            chunk_id:       0,
                            fastq_id:       "dimitri_TCR",
                            fastqs: {
                                "i1": null,
                                "i2": null,
                                "r1": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R1_001.fastq.gz",
                                "r1_interleaved": false,
                                "r2": "/scratch/etanis/ST-118/FASTQ/dimitri_TCR_S1_L001_R2_001.fastq.gz",
                            },
                            gem_group:      1,
                            library_id:     0,
                            library_type:   "VDJ",
                            read_group:     "dimitri-multi:0:1:HKLTCBGXL:1",
                            read_lengths:   {},
                            subsample_rate: null,
                        },
                    ],
                },
            },
        },
        multi_metrics_csvs: {
            dimitri-multi: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/BUILD_MULTI_WEB_SUMMARY/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_metrics_summary.csv",
        },
        multi_reporter: {
            antibody_histograms:    null,
            barcode_rank_plots: {
                Gene Expression: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS/fork0/chnk0-ucc6a7a7d79/files/Gene Expression_barcode_rank_plot.json",
            },
            cloupe:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0-ucc6a7a7dbf/files/cloupe.cloupe",
            cmo_tsne_plot:          null,
            count_summary: {
                feature_reference:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ucc6a7a7d79/files/feature_reference.csv",
                metrics_summary_csv:  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ucc6a7a7d79/files/metrics_summary_csv.csv",
                metrics_summary_json: "/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",
                web_summary:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ucc6a7a7d79/files/web_summary.html",
                ws_data:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ucc6a7a7d79/files/ws_data.json",
            },
            jibes_biplot_histogram: null,
            vdj_b_report: {
                annotations_bed:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/annotations_bed.bed",
                cell_barcodes:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/cell_barcodes.json",
                contig_fasta:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fasta.fasta",
                contig_fasta_fai:         "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fasta.fasta.fai",
                contig_fastq:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fastq.fastq",
                filtered_contig_fasta:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_fasta.fasta",
                filtered_contig_fastq:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_fastq.fastq",
                metrics_summary_csv:      "/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_csv.csv",
                metrics_summary_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/metrics_summary_json.json",
                productive_cell_barcodes: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/paired_cell_barcodes.json",
                receptor:                 "IG",
                vdj_contig_info:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_PROTO/fork0/chnk0-ucc6a7a7cea/files/vdj_contig_info.pb",
                vloupe:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/VLOUPE_PREPROCESS/fork0/chnk0-ucc6a7a7cd7/files/output_for_vloupe.vloupe",
                web_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/web_summary.html",
                web_summary_data:         "/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_t_report: {
                annotations_bed:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/annotations_bed.bed",
                cell_barcodes:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/cell_barcodes.json",
                contig_fasta:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fasta.fasta",
                contig_fasta_fai:         "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fasta.fasta.fai",
                contig_fastq:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fastq.fastq",
                filtered_contig_fasta:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_fasta.fasta",
                filtered_contig_fastq:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_fastq.fastq",
                metrics_summary_csv:      "/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_csv.csv",
                metrics_summary_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/metrics_summary_json.json",
                productive_cell_barcodes: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/paired_cell_barcodes.json",
                receptor:                 "TR",
                vdj_contig_info:          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_PROTO/fork0/chnk0-ucc6a7a7ce7/files/vdj_contig_info.pb",
                vloupe:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/VLOUPE_PREPROCESS/fork0/chnk0-ucc6a7a7cd5/files/output_for_vloupe.vloupe",
                web_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/web_summary.html",
                web_summary_data:         "/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",
            },
        },
        multi_web_summaries: {
            dimitri-multi: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/BUILD_MULTI_WEB_SUMMARY/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_web_summary.html",
        },
        multi_web_summary_json: {
            metrics_summary_csv: {
                dimitri-multi: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/WRITE_MULTI_WEB_SUMMARY_JSON/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_metric_summary_csv.json.csv",
            },
            web_summary_json: {
                dimitri-multi: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/WRITE_MULTI_WEB_SUMMARY_JSON/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_web_summary_data.json",
            },
        },
        sample_analyzer: {
            dimitri-multi: {
                antibody_analyzer: null,
                crispr_analyzer:   null,
                rna_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",
                },
                targeted_analyzer: null,
            },
        },
        sample_outs: {
            dimitri-multi: {
                "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_reporter: {
            dimitri-multi: {
                cloupe:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/join-ucc6a7a7db5/files/output_for_cloupe.cloupe",
                metrics_summary:   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/_SAMPLE_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork_dimitri-multi/join-ucc6a7a7db3/files/summary.json",
                sample_tsne_plots: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/GENERATE_SAMPLE_TSNE_PLOTS/fork_dimitri-multi/join-ucc6a7a7d8f/files/sample_tsne_plots.json",
                vdj_b_report:      null,
                vdj_t_report:      null,
            },
        },
        split_vdj: {
            vdj_b_chemistry_type: "SCVDJ-R2",
            vdj_b_input: {
                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,
            },
            vdj_b_receptor:       "IG",
            vdj_t_chemistry_type: "SCVDJ-R2",
            vdj_t_input: {
                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_receptor:       "TR",
        },
        unassigned_bai: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_unassigned.bam.bai",
        unassigned_bam: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_unassigned.bam",
        vdj_b_clonotype: {
            airr_rearrangement:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/chnk0-ucc6a7a7ce7/files/airr_annotations.tsv",
            all_contig_annotations_csv:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd8/files/all_contig_annotations.csv",
            all_contig_annotations_json:     "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/HANDLE_NO_VDJ_REF/fork0/chnk0-ucc6a7a7cd8/files/all_contig_annotations.json",
            clonotypes_csv:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/chnk0-ucc6a7a7cd7/files/clonotypes.csv",
            concat_ref_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.bam",
            concat_ref_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.bam.bai",
            concat_ref_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.fasta",
            concat_ref_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.fasta.fai",
            consensus_annotations_csv:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus_annotations.csv",
            consensus_bam:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd8/files/consensus.bam",
            consensus_bam_bai:               "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd8/files/consensus.bam.bai",
            consensus_fasta:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus.fasta",
            consensus_fasta_fai:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus.fasta.fai",
            disable_vloupe:                  false,
            donor_ref_fa:                    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7cce/files/donor_ref.fa",
            enclone_output:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7cce/files/enclone_output.pb",
            filtered_contig_annotations_csv: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_annotations.csv",
            summary:                         "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7cce/files/summary.json",
        },
        vdj_ref_out: {
            fasta: {
                "donor_regions": "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0/chnk0-ucc6a7a7cd7/files/donor_regions.fa",
                "regions": "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0/chnk0-ucc6a7a7cd7/files/regions.fa",
            },
            reference: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0/chnk0-ucc6a7a7cd7/files/reference.json",
        },
        vdj_t_clonotype: {
            airr_rearrangement:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/chnk0-ucc6a7a7cdd/files/airr_annotations.tsv",
            all_contig_annotations_csv:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd7/files/all_contig_annotations.csv",
            all_contig_annotations_json:     "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/HANDLE_NO_VDJ_REF/fork0/chnk0-ucc6a7a7cd7/files/all_contig_annotations.json",
            clonotypes_csv:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/chnk0-ucc6a7a7cd5/files/clonotypes.csv",
            concat_ref_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.bam",
            concat_ref_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.bam.bai",
            concat_ref_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.fasta",
            concat_ref_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.fasta.fai",
            consensus_annotations_csv:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus_annotations.csv",
            consensus_bam:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd7/files/consensus.bam",
            consensus_bam_bai:               "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd7/files/consensus.bam.bai",
            consensus_fasta:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus.fasta",
            consensus_fasta_fai:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus.fasta.fai",
            disable_vloupe:                  false,
            donor_ref_fa:                    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7ccd/files/donor_ref.fa",
            enclone_output:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7ccd/files/enclone_output.pb",
            filtered_contig_annotations_csv: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_annotations.csv",
            summary:                         "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/chnk0-ucc6a7a7ccd/files/summary.json",
        },
    },
)
