@include "atac/_sc_atac_reporter_stages.mro"

call CREATE_WEBSUMMARY(
    reference_path          = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    barcode_whitelist       = "737K-arc-v1",
    summary_results         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u3b7f6eb7d3/files/summary.json",
    bulk_complexity         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u3b7f6eb4ba/files/bulk_complexity.json",
    singlecell_complexity   = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u3b7f6eb4ba/files/singlecell_complexity.json",
    sample_id               = "pbmc_granulocyte_sorted_10k",
    sample_desc             = "pbmc_granulocyte_sorted_10k",
    sample_def              = [
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Chromatin Accessibility",
            "read_path": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac",
            "sample_indices": ["any"],
            "sample_names": ["pbmc_granulocyte_sorted_10k"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    debug                   = false,
    peak_qval               = null,
    singlecell              = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u3b7f6eb6ce/files/singlecell.csv",
    insert_sizes            = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/insert_sizes.csv",
    tss_relpos              = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u3b7f6eafbe/files/tss.csv",
    ctcf_relpos             = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u3b7f6eafbe/files/ctcf.csv",
    filtered_peak_bc_matrix = "/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",
    analysis                = null,
    excluded_barcodes       = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u3b7f6eb4a5/files/excluded_barcodes.json",
    count_dict              = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u3b7f6eab43/files/count_dict.json",
)
