@include "rna/_common_stages.mro"

call DISABLE_FEATURE_STAGES(
    sample_def          = [
        {
            "fastq_id": "dimitri_RNA",
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": 1,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/scratch/etanis/ST-118/FASTQ/",
            "sample_indices": null,
            "sample_names": ["dimitri_RNA"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    disable_multi       = false,
    disable_count       = false,
    is_pd               = false,
    in_disable_targeted = true,
    sample_outs         = {
        "dimitri-multi": {
            all_genes_matrix_h5:  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix.h5",
            all_genes_matrix_mex: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_all_genes_filtered_feature_barcode_matrix",
            bam_file:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_dimitri-multi.bam",
            bam_index_file:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/pos_sorted_dimitri-multi.bam.bai",
            feature_reference:    null,
            filtered_barcodes:    "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_barcodes.csv",
            matrix_h5:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix.h5",
            matrix_mex:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix",
            metrics_summary:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_summary.json",
            molecule_info:        "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/molecule_info_dimitri-multi.h5",
            per_barcode_metrics:  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_per_barcode_metrics.csv",
            sample:               "dimitri-multi",
            target_panel:         null,
        },
    },
    multi_graph         = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/PARSE_MULTI_CONFIG/fork0/chnk0-ucc6a7a7197/files/multi_graph.json",
)
