@include "atac_rna/_joint_cell_detector.mro"

call _JOINT_CELL_DETECTOR(
    sample_id             = "count-NYU070",
    reference_path        = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    barcode_whitelist     = "737K-arc-v1",
    rna_raw_matrix        = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u45960dd236/files/raw_feature_bc_matrix.h5",
    atac_raw_matrix       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u45960ddf9a/files/raw_matrix.h5",
    peaks                 = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u45960ddab2/files/peaks.bed",
    fragments             = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u45960dc732/files/fragments.tsv.gz",
    fragments_index       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u45960dc732/files/fragments.tsv.gz.tbi",
    force_cells           = null,
    rna_gem_groups        = [1],
    disable_bc_multiplets = true,
)
