@include "atac_rna/_sc_atac_gex_analyzer_stages.mro"

call ATAC_GEX_SUMMARIZE_ANALYSIS(
    matrix                     = {
        atac:     "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u3b7f6eb558/files/atac.h5",
        atac_gex: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u3b7f6eb558/files/atac_gex.h5",
        gex:      "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u3b7f6eb558/files/gex.h5",
    },
    tf_propZ_matrix            = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u3b7f6eb902/files/tf_propZ_matrix.gz",
    peak_annotation            = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u3b7f6eb8a8/files/peak_annotation.tsv",
    reduced_data               = {
        atac: {
            method:     "lsa",
            num_dims:   15,
            projection: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u3b7f6eb8a8/files/reduced_data",
        },
        atac_gex: null,
        gex: {
            method:     "pca",
            num_dims:   10,
            projection: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u3b7f6eb8a8/files/reduced_data",
        },
    },
    tsne                       = {
        atac:     "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u3b7f6eb935/files/projection_output",
        atac_gex: null,
        gex:      "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u3b7f6eb8c1/files/projection_output",
    },
    umap                       = {
        atac:     "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u3b7f6eb935/files/projection_output",
        atac_gex: null,
        gex:      "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u3b7f6eb8c1/files/projection_output",
    },
    clustering                 = {
        atac:     "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u3b7f6eb946/files/clustering",
        atac_gex: null,
        gex:      "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u3b7f6eb8d1/files/clustering",
    },
    differential_expression    = {
        atac: {
            csv: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u3b7f6eb946/files/diffexp_csv",
            h5:  "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u3b7f6eb946/files/diffexp_h5.h5",
        },
        atac_gex: null,
        gex: {
            csv: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u3b7f6eb8f9/files/diffexp_csv",
            h5:  "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u3b7f6eb8f9/files/diffexp_h5.h5",
        },
    },
    differential_accessibility = {
        atac:     "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u3b7f6eb94a/files/enrichment_analysis",
        atac_gex: null,
        gex:      "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u3b7f6eb94a/files/enrichment_analysis",
    },
    filtered_tf_bc_matrix_h5   = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u3b7f6eb902/files/filtered_tf_bc_matrix.h5",
    max_clusters               = null,
    feature_linkage            = {
        feature_linkage:        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u3b7f6eb950/files/feature_linkage.bedpe",
        feature_linkage_matrix: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u3b7f6eb950/files/feature_linkage_matrix.h5",
    },
)
