@include "rna/sc_rna_counter_cs.mro"

call _STRUCTIFY(
    common_input = {
        multi_config_sha: null,
        sample_desc:      "",
        sample_id:        "dimitri_RNA_only",
    },
    count_input  = {
        aligner:                   null,
        cell_calling_config: {
            cell_barcodes:                  null,
            disable_ab_aggregate_detection: false,
            force_cells:                    null,
            override_library_types:         null,
            override_mode:                  null,
            recovered_cells:                null,
        },
        chemistry:                 "auto",
        feature_reference:         null,
        force_sample_barcodes:     null,
        gene_index:                "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/chnk0-ufc475ecb80/files/gene_index.json",
        include_introns:           false,
        min_assignment_confidence: null,
        no_bam:                    false,
        no_secondary_analysis:     false,
        no_target_umi_filter:      false,
        r1_length:                 null,
        r2_length:                 null,
        reference_path:            "/scratch/etanis/refs/10x_ref/refdata-gex-GRCh38-2020-A",
        sample_def: [
            {
                "fastq_id": null,
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": null,
                "lanes": null,
                "library_type": "Gene Expression",
                "read_path": "/scratch/etanis/ST-118/FASTQ/",
                "sample_indices": ["any"],
                "sample_names": ["dimitri_RNA"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
        targeting_method:          null,
        tenx_cmos:                 null,
        trim_polya_min_score:      20,
        trim_tso_min_score:        20,
    },
    config       = {
        disable_count:       false,
        disable_multi:       true,
        disable_multi_count: true,
        disable_vdj:         true,
    },
)
