@include "atac/_cr_atac_stages.mro"

call MARK_ATAC_DUPLICATES(
    aligned_shards   = [
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud1886f6efd/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk30-ud1886f6efe/files/aligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk31-ud1886f6eff/files/aligned_chunk.shard",
    ],
    unaligned_shards = [
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-ud1886f6efd/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk30-ud1886f6efe/files/unaligned_chunk.shard",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk31-ud1886f6eff/files/unaligned_chunk.shard",
    ],
    num_read_pairs   = 310036087,
    reference_path   = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    barcode_counts   = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-ud1886f6d62/files/barcode_counts.bch.bincode",
    assay            = "arc",
    sample_id        = "human_brain_3k",
    sample_desc      = "human_brain_3k",
)
