@include "atac_rna/_sc_atac_gex_analyzer.mro"

call _CLUSTER_COMPUTER_CORE as _GEX_CLUSTERING_COMPUTER(
    reduced_data          = {
        method:     "pca",
        num_dims:   10,
        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",
    },
    matrix_clustering     = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u45960deb66/files/gex.h5",
    reference_path        = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    peaks                 = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u45960ddab2/files/peaks.bed",
    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.h5",
    matrix                = {
        atac:     "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u45960deb66/files/atac.h5",
        atac_gex: "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u45960deb66/files/atac_gex.h5",
        gex:      "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u45960deb66/files/gex.h5",
    },
    max_clusters          = null,
    random_seed           = null,
    neighbor_a            = null,
    neighbor_b            = null,
    graphclust_neighbors  = null,
)
