@include "rna/_cr_lib_stages.mro"

call WRITE_MATRIX_MARKET(
    gem_well          = 1,
    counts            = [
        "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk0-udc993dad9f/files/bc_sort.csf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk1-udc993dad9f/files/bc_sort.csf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk2-udc993dad9f/files/bc_sort.csf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk3-udc993dad9f/files/bc_sort.csf",
        "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk4-udc993dad9f/files/bc_sort.csf",
    ],
    bcs               = "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-udc993dad99/files/correct_barcode_counts.bcc.bincode",
    barcode_whitelist = "visium-v1",
    feature_reference = "/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-udc993dac80/files/feature_reference.frf.bincode",
)
