@include "atac_rna/_feature_linkage_computer_stages.mro"

call COMPUTE_FEATURE_LINKAGES(
    merged_filtered_matrix_h5 = "/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",
    atac_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",
    reference_path            = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    feature_grouping          = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u3b7f6eb936/files/feature_grouping.pkl",
    barcode_metadata          = {
        depth_scale_factors: "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u3b7f6eb936/files/depth_scale_factors.csv",
        similarity_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/PREPROCESS_JOINT_MATRIX/fork0/join-u3b7f6eb936/files/similarity_matrix.h5",
        smoothing_weights:   "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u3b7f6eb936/files/smoothing_weights.h5",
    },
    max_dist_mb               = null,
)
