@include "rna/_common_stages.mro"

call PARSE_TARGET_FEATURES(
    sample_def           = [
        {
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A",
            "sample_indices": ["any"],
            "sample_names": ["BS20957A"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    reference_path       = "/gpfs/data/yanailab/refs/homo_sapiens/hg38_mm10_10X/hg38_and_mm10",
    gene_index           = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/WRITE_GENE_INDEX/fork0/chnk0-ufe8a67f4d3/files/gene_index.json",
    no_target_umi_filter = true,
    rps_limit            = null,
)
