@include "rna/_cr_lib_stages.mro"

call COLLATE_METRICS(
    per_barcode_metrics  = [
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u4c9f5eb328/files/metrics_shard.bmsf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u4c9f5eb328/files/metrics_shard.bmsf",
    ],
    reference_path       = "/scratch/etanis/refs/10x_ref/refdata-gex-GRCh38-2020-A",
    feature_reference    = "/scratch/etanis/software/cellranger-6.1.2/dimitri/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u4c9f5ead77/files/feature_reference.frf.bincode",
    sample_barcodes_json = null,
)
