@include "atac_rna/reporter_stages.mro"

call CREATE_JOINT_WEBSUMMARY(
    reference_path              = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    sample_id                   = "count-NYU070",
    sample_desc                 = "count-NYU070",
    merge_singlecell            = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u45960df83d/files/metrics.csv",
    summary                     = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u45960df83d/files/summary.json",
    atac_data                   = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u45960df053/files/data.json",
    gex_data                    = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u45960deff0/files/ws_data.json",
    analysis_csv                = {
        clustering: {
            atac: {
                "graphclust": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df3fa/files/clustering/lsa/lsa_csv/graphclust/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df519/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df519/files/diffexp_csv/graphclust/differential_expression.csv",
                },
                "kmeans_2_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df3fa/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df519/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df519/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                },
                "kmeans_3_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df3fa/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df519/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df519/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                },
                "kmeans_4_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df3fa/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df519/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df519/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                },
                "kmeans_5_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df3fa/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df519/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df519/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                },
            },
            gex: {
                "graphclust": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df03d/files/clustering/pca/pca_csv/graphclust/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df06e/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df03f/files/diffexp_csv/graphclust/differential_expression.csv",
                },
                "kmeans_2_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df03d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df06e/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df03f/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv",
                },
                "kmeans_3_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df03d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df06e/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df03f/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv",
                },
                "kmeans_4_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df03d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df06e/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df03f/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv",
                },
                "kmeans_5_clusters": {
                    "clusters": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u45960df03d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv",
                    "differential_accessibility": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u45960df06e/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv",
                    "differential_expression": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u45960df03f/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv",
                },
            },
        },
        dimensionality_reduction: {
            atac: {
                "lsa_components": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/lsa/lsa_csv/15_components/components.csv",
                "lsa_dispersion": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv",
                "lsa_features_selected": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv",
                "lsa_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/lsa/lsa_csv/15_components/projection.csv",
                "lsa_variance": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/lsa/lsa_csv/15_components/variance.csv",
                "tsne_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u45960df3be/files/projection_output/lsa_tsne_csv/2_components/projection.csv",
                "umap_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u45960df3be/files/projection_output/lsa_umap_csv/2_components/projection.csv",
            },
            gex: {
                "pca_components": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/pca/pca_csv/10_components/components.csv",
                "pca_dispersion": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/pca/pca_csv/10_components/dispersion.csv",
                "pca_features_selected": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/pca/pca_csv/10_components/features_selected.csv",
                "pca_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/pca/pca_csv/10_components/projection.csv",
                "pca_variance": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u45960deff0/files/reduced_data/pca/pca_csv/10_components/variance.csv",
                "tsne_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u45960df028/files/projection_output/pca_tsne_csv/2_components/projection.csv",
                "umap_projection": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u45960df028/files/projection_output/pca_umap_csv/2_components/projection.csv",
            },
        },
        feature_linkage: {
            feature_linkage:        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u45960df3e1/files/feature_linkage.bedpe",
            feature_linkage_matrix: "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u45960df3e1/files/feature_linkage_matrix.h5",
        },
        tf_analysis: {
            filtered_tf_bc_matrix:    "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u45960df02d/files/filtered_tf_bc_matrix_mex",
            filtered_tf_bc_matrix_h5: "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u45960df02d/files/filtered_tf_bc_matrix.h5",
            peak_motif_mapping:       "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u45960df004/files/peak_motif_hits.bed",
        },
    },
    debug                       = false,
    rna_include_introns         = true,
    atac_peak_qval              = null,
    feature_linkage_max_dist_mb = null,
)
