@include "atac_rna/sc_atac_gex_counter.mro"

call SC_ATAC_GEX_COUNTER(
    gem_well                    = 1,
    sample_id                   = "pbmc_granulocyte_sorted_10k",
    sample_desc                 = "pbmc_granulocyte_sorted_10k",
    sample_def                  = [
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/gex",
            "sample_indices": ["any"],
            "sample_names": ["pbmc_granulocyte_sorted_10k"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Chromatin Accessibility",
            "read_path": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac",
            "sample_indices": ["any"],
            "sample_names": ["pbmc_granulocyte_sorted_10k"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    reference_path              = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    force_cells                 = null,
    skip_compatibility_check    = false,
    feature_linkage_max_dist_mb = null,
    k_means_max_clusters        = null,
    no_bam                      = false,
    rna_chemistry               = "ARC-v1",
    rna_custom_chemistry_def    = null,
    rna_recovered_cells         = 1000,
    rna_subsample_rate          = 1,
    rna_initial_reads           = null,
    rna_r1_length               = null,
    rna_r2_length               = null,
    rna_feature_reference       = null,
    rna_include_introns         = true,
    rna_trim_polya_min_score    = 20,
    rna_trim_tso_min_score      = 20,
    atac_subsample_rate         = null,
    atac_barcode_whitelist      = "737K-arc-v1",
    atac_custom_peaks           = null,
    atac_peak_qval              = null,
    disable_bc_multiplets       = true,
)
