@include "rna/sc_multi_core.mro"

call BUILD_SAMPLE_OUTS(
    sample_slfe_outs    = {
        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,
    },
    rna_analysis        = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SANITIZE_MAP_CALLS/fork0/chnk0-ucc6a7a7dbf/files/dimitri-multi_analysis_csv",
    crispr_analysis     = null,
    antibody_analysis   = null,
    cloupe              = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SANITIZE_MAP_CALLS/fork0/chnk0-ucc6a7a7dbf/files/dimitri-multi_output_for_cloupe.cloupe",
    web_summary         = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/BUILD_MULTI_WEB_SUMMARY/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_web_summary.html",
    metrics_summary_csv = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/BUILD_MULTI_WEB_SUMMARY/fork0/chnk0-ucc6a7a7db6/files/dimitri-multi_metrics_summary.csv",
    vdj_b_outs          = {
        airr_rearrangement:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/chnk0-ucc6a7a7ce7/files/airr_annotations.tsv",
        all_contig_annotations_bed:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/annotations_bed.bed",
        all_contig_annotations_csv:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd8/files/all_contig_annotations.csv",
        all_contig_annotations_json:     "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/HANDLE_NO_VDJ_REF/fork0/chnk0-ucc6a7a7cd8/files/all_contig_annotations.json",
        all_contig_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/contig_bam.bam",
        all_contig_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72ce/files/contig_bam.bam.bai",
        all_contig_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fasta.fasta",
        all_contig_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fasta.fasta.fai",
        all_contig_fastq:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/contig_fastq.fastq",
        cell_barcodes:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/cell_barcodes.json",
        clonotypes:                      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/chnk0-ucc6a7a7cd7/files/clonotypes.csv",
        concat_ref_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.bam",
        concat_ref_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.bam.bai",
        concat_ref_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.fasta",
        concat_ref_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd8/files/concat_ref.fasta.fai",
        consensus_annotations_csv:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus_annotations.csv",
        consensus_bam:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd8/files/consensus.bam",
        consensus_bam_bai:               "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd8/files/consensus.bam.bai",
        consensus_fasta:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus.fasta",
        consensus_fasta_fai:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd7/files/consensus.fasta.fai",
        filtered_contig_annotations_csv: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_B_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_annotations.csv",
        filtered_contig_fasta:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_fasta.fasta",
        filtered_contig_fastq:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd8/files/filtered_contig_fastq.fastq",
        metrics_summary_csv:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce4/files/metrics_summary_csv.csv",
        vdj_contig_info:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/WRITE_CONTIG_PROTO/fork0/chnk0-ucc6a7a7cea/files/vdj_contig_info.pb",
        vloupe:                          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_B_REPORTER/VLOUPE_PREPROCESS/fork0/chnk0-ucc6a7a7cd7/files/output_for_vloupe.vloupe",
    },
    vdj_t_outs          = {
        airr_rearrangement:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/chnk0-ucc6a7a7cdd/files/airr_annotations.tsv",
        all_contig_annotations_bed:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/annotations_bed.bed",
        all_contig_annotations_csv:      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd7/files/all_contig_annotations.csv",
        all_contig_annotations_json:     "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/HANDLE_NO_VDJ_REF/fork0/chnk0-ucc6a7a7cd7/files/all_contig_annotations.json",
        all_contig_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/contig_bam.bam",
        all_contig_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join-ucc6a7a72e6/files/contig_bam.bam.bai",
        all_contig_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fasta.fasta",
        all_contig_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fasta.fasta.fai",
        all_contig_fastq:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/contig_fastq.fastq",
        cell_barcodes:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/cell_barcodes.json",
        clonotypes:                      "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/chnk0-ucc6a7a7cd5/files/clonotypes.csv",
        concat_ref_bam:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.bam",
        concat_ref_bam_bai:              "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.bam.bai",
        concat_ref_fasta:                "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.fasta",
        concat_ref_fasta_fai:            "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/chnk0-ucc6a7a7cd7/files/concat_ref.fasta.fai",
        consensus_annotations_csv:       "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus_annotations.csv",
        consensus_bam:                   "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd7/files/consensus.bam",
        consensus_bam_bai:               "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/chnk0-ucc6a7a7cd7/files/consensus.bam.bai",
        consensus_fasta:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus.fasta",
        consensus_fasta_fai:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/chnk0-ucc6a7a7cd5/files/consensus.fasta.fai",
        filtered_contig_annotations_csv: "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/VDJ_T_CLONOTYPE_ASSIGNER/CLONOTYPE_ASSIGNER/WRITE_ANN_CSV/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_annotations.csv",
        filtered_contig_fasta:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_fasta.fasta",
        filtered_contig_fastq:           "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_OUTS/fork0/chnk0-ucc6a7a7cd7/files/filtered_contig_fastq.fastq",
        metrics_summary_csv:             "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/SUMMARIZE_VDJ_REPORTS/fork0/join-ucc6a7a7ce0/files/metrics_summary_csv.csv",
        vdj_contig_info:                 "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/WRITE_CONTIG_PROTO/fork0/chnk0-ucc6a7a7ce7/files/vdj_contig_info.pb",
        vloupe:                          "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_REPORTER/VDJ_T_REPORTER/VLOUPE_PREPROCESS/fork0/chnk0-ucc6a7a7cd5/files/output_for_vloupe.vloupe",
    },
)
