@include "atac_rna/_sc_atac_gex_analyzer.mro"

call _SC_ATAC_GEX_ANALYZER(
    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",
    },
    method                      = {
        atac:     "lsa",
        atac_gex: "pca",
        gex:      "pca",
    },
    projection_dims             = {
        atac:     15,
        atac_gex: 15,
        gex:      10,
    },
    random_seed                 = null,
    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",
    max_clusters                = null,
    feature_linkage_max_dist_mb = null,
    linkage_projection          = null,
)
