@include "rna/_cr_lib_stages.mro"

call COLLATE_METRICS(
    per_barcode_metrics = [
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk0-ue5873daf48/files/metrics_shard.bmsf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk1-ue5873daf48/files/metrics_shard.bmsf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk2-ue5873daf48/files/metrics_shard.bmsf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk3-ue5873daf48/files/metrics_shard.bmsf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk4-ue5873daf48/files/metrics_shard.bmsf",
    ],
    reference_path      = "/gpfs/data/yanailab/refs/mus_musculus/refdata-gex-mm10-2020-A_JY",
    feature_reference   = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ue5873dae13/files/feature_reference.frf.bincode",
)
