@include "atac/_sc_atac_reporter_stages.mro"

call CREATE_WEBSUMMARY(
    reference_path          = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    barcode_whitelist       = "737K-arc-v1",
    summary_results         = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u45960df051/files/summary.json",
    bulk_complexity         = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u45960dea93/files/bulk_complexity.json",
    singlecell_complexity   = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u45960dea93/files/singlecell_complexity.json",
    sample_id               = "count-NYU070",
    sample_desc             = "count-NYU070",
    sample_def              = [
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Chromatin Accessibility",
            "read_path": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/",
            "sample_indices": ["any"],
            "sample_names": ["NYU070_ATAC"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    debug                   = false,
    peak_qval               = null,
    singlecell              = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u45960dede8/files/singlecell.csv",
    insert_sizes            = "/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/MARK_ATAC_DUPLICATES/fork0/join-u45960dc732/files/insert_sizes.csv",
    tss_relpos              = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u45960ddf9a/files/tss.csv",
    ctcf_relpos             = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u45960ddf9a/files/ctcf.csv",
    filtered_peak_bc_matrix = "/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",
    analysis                = null,
    excluded_barcodes       = "/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_EXCLUDED_BARCODES/fork0/chnk0-u45960de7df/files/excluded_barcodes.json",
    count_dict              = "/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/COUNT_CUT_SITES/fork0/chnk0-u45960dd9f7/files/count_dict.json",
)
