@include "sc_rna_counter_cs.mro"

call SC_RNA_COUNTER_CS(
    sample_id = "10X_G171B_pcg_only_UseThis",
    sample_def = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "read_path": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/H3LTJBBXX/10X_G171B_MissingLibrary_1_H3LTJBBXX",
            "sample_indices": [
                "any"
            ],
            "sample_names": [
                "G171B"
            ]
        }
    ],
    sample_desc = "",
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_v1.0_pcg-only",
    recovered_cells = 5000,
    no_secondary_analysis = false,
    force_cells = null,
    chemistry = "auto",
    r1_length = null,
    r2_length = null,
    feature_reference = null,
)