@include "atac_rna/_fastq_stager.mro"

call _FASTQ_STAGER(
    sample_id                = "pbmc_granulocyte_sorted_10k",
    atac_sample_def          = [
        {
            "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,
        },
    ],
    atac_barcode_whitelist   = "737K-arc-v1",
    atac_subsample_rate      = null,
    rna_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,
        },
    ],
    rna_chemistry            = "ARC-v1",
    rna_custom_chemistry_def = null,
)
