atac.croo.json

{
  "atac.jsd": {
    "plot": {
      "path": "qc/${basename}",
      "table": "QC and logs/Jensen-Shannon distance plot",
      "node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"JSD\nPlot\"]"
    }
  },
  "atac.frac_mito": {
    "frac_mito_qc": {
      "path": "qc/${basename}",
      "table": "QC and logs/Fraction of mitochondrial reads in raw BAM"
    }
  },
  "atac.bowtie2": {
    "bam": {
      "path": "align/rep${i+1}/${basename}",
      "table": "Alignment/Replicate ${i+1}/Raw BAM from bowtie2"
    },
    "flagstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Samtools flagstat for Raw BAM"
    },
    "read_len_log": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Read length"
    }
  },
  "atac.align": {
    "bam": {
      "path": "align/rep${i+1}/${basename}",
      "table": "Alignment/Replicate ${i+1}/Raw BAM from aligner",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"BAM\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "flagstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Samtools flagstat for Raw BAM"
    },
    "samstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/SAMstats log for Raw BAM",
      "node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"SAMstats\nQC\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "read_len_log": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Read length"
    }
  },
  "atac.filter": {
    "nodup_bam": {
      "path": "align/rep${i+1}/${basename}",
      "table": "Alignment/Replicate ${i+1}/Filtered BAM",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Filt/deduped\nBAM\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "flagstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Samtools flagstat log for filtered BAM"
    },
    "samstat_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/SAMstats log for filtered BAM",
      "node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"SAMstats\nQC\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "dup_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Dup QC for filtered BAM"
    },
    "pbc_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/PBC QC for filtered BAM",
      "subgraph": "cluster_rep${i+1}"
    },
    "lib_complexity_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Library complexity QC for filtered BAM",
      "node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"LibCmplx\nQC\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "mito_dup_log": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Mito dup log for filtered BAM"
    }
  },
  "atac.bam2ta": {
    "ta": {
      "path": "align/rep${i+1}/${basename}",
      "table": "Alignment/Replicate ${i+1}/TAG-ALIGN",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"TAG-ALIGN\"]",
      "subgraph": "cluster_rep${i+1}"
    }
  },
  "atac.spr": {
    "ta_pr1": {
      "path": "align/rep${i+1}/pseudorep1/${basename}",
      "table": "Alignment/Replicate ${i+1}/Pseudoreplicate 1/TAG-ALIGN"
    },
    "ta_pr2": {
      "path": "align/rep${i+1}/pseudorep2/${basename}",
      "table": "Alignment/Replicate ${i+1}/Pseudoreplicate 2/TAG-ALIGN"
    }
  },
  "atac.pool_ta": {
    "ta_pooled": {
      "path": "align/pooled-rep/${basename}",
      "table": "Alignment/Pooled replicate/TAG-ALIGN",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"TAG-ALIGN\"]",
      "subgraph": "cluster_pooled_rep"
    }
  },
  "atac.pool_ta_pr1": {
    "ta_pooled": {
      "path": "align/pooled-rep/pseudorep1/${basename}",
      "table": "Alignment/Pooled replicate/Pseudoreplicate 1/TAG-ALIGN"
    }
  },
  "atac.pool_ta_pr2": {
    "ta_pooled": {
      "path": "align/pooled-rep/pseudorep2/${basename}",
      "table": "Alignment/Pooled replicate/Pseudoreplicate 2/TAG-ALIGN"
    }
  },
  "atac.xcor": {
    "plot_png": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Cross-correlation Plot",
      "node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"XCOR\nPlot\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "score": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Cross-correlation score"
    },
    "fraglen": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Estimated fragment length"
    }
  },
  "atac.macs2": {
    "npeak": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.macs2_pr1": {
    "npeak": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/pseudorep1/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Pseudoreplicate 1/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.macs2_pr2": {
    "npeak": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/pseudorep2/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Pseudoreplicate 2/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.macs2_pooled": {
    "npeak": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/${basename}",
      "table": "QC and logs/Pooled replicate/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.macs2_ppr1": {
    "npeak": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/pseudorep1/${basename}",
      "table": "QC and logs/Pooled replicate/Pseudoreplicate 1/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.macs2_ppr2": {
    "npeak": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Raw MACS2 narrowpeak"
    },
    "bfilt_npeak": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak"
    },
    "bfilt_npeak_bb": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak (BigBed)"
    },
    "bfilt_npeak_hammock": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered MACS2 narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/pseudorep2/${basename}",
      "table": "QC and logs/Pooled replicate/Pseudoreplicate 2/Fraction of MACS2 peaks in reads"
    }
  },
  "atac.call_peak": {
    "peak": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Raw narrowpeak",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Peak\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "bfilt_peak": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Peak\n(bfilt)\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "bfilt_peak_bb": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/rep${i+1}/${basename}",
      "table": "Peak/Replicate ${i+1}/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Fraction of peaks in reads"
    }
  },
  "atac.call_peak_pr1": {
    "peak": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Raw narrowpeak"
    },
    "bfilt_peak": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak"
    },
    "bfilt_peak_bb": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/rep${i+1}/pseudorep1/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 1/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/pseudorep1/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Pseudoreplicate 1/Fraction of peaks in reads"
    }
  },
  "atac.call_peak_pr2": {
    "peak": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Raw narrowpeak"
    },
    "bfilt_peak": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak"
    },
    "bfilt_peak_bb": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/rep${i+1}/pseudorep2/${basename}",
      "table": "Peak/Replicate ${i+1}/Pseudoreplicate 2/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/rep${i+1}/pseudorep2/${basename}",
      "table": "QC and logs/Replicate ${i+1}/Pseudoreplicate 2/Fraction of peaks in reads"
    }
  },
  "atac.call_peak_pooled": {
    "peak": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Raw narrowpeak",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Peak\"]",
      "subgraph": "cluster_pooled_rep"
    },
    "bfilt_peak": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Peak\n(bfilt)\"]",
      "subgraph": "cluster_pooled_rep"
    },
    "bfilt_peak_bb": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/pooled-rep/${basename}",
      "table": "Peak/Pooled replicate/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/${basename}",
      "table": "QC and logs/Pooled replicate/Fraction of peaks in reads"
    }
  },
  "atac.call_peak_ppr1": {
    "peak": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Raw narrowpeak"
    },
    "bfilt_peak": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak"
    },
    "bfilt_peak_bb": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/pooled-rep/pseudorep1/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 1/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/pseudorep1/${basename}",
      "table": "QC and logs/Pooled replicate/Pseudoreplicate 1/Fraction of peaks in reads"
    }
  },
  "atac.call_peak_ppr2": {
    "peak": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Raw narrowpeak"
    },
    "bfilt_peak": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak"
    },
    "bfilt_peak_bb": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak (BigBed)"
    },
    "bfilt_peak_hammock": {
      "path": "peak/pooled-rep/pseudorep2/${basename}",
      "table": "Peak/Pooled replicate/Pseudoreplicate 2/Blacklist-filtered narrowpeak (hammock)"
    },
    "frip_qc": {
      "path": "qc/pooled-rep/pseudorep2/${basename}",
      "table": "QC and logs/Pooled replicate/Pseudoreplicate 2/Fraction of peaks in reads"
    }
  },
  "atac.macs2_signal_track": {
    "pval_bw": {
      "path": "signal/rep${i+1}/${basename}",
      "table": "Signal/Replicate ${i+1}/MACS2 signal track (p-val)",
      "ucsc_track": "track type=bigWig name=\"MACS2 p-val (rep${i+1})\" priority=${i+1} smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"BW\np-val\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "fc_bw": {
      "path": "signal/rep${i+1}/${basename}",
      "table": "Signal/Replicate ${i+1}/MACS2 signal track (fold-enrichment)",
      "ucsc_track": "track type=bigWig name=\"MACS2 fc (rep${i+1})\" priority=${i+1} smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"BW\nFC\"]",
      "subgraph": "cluster_rep${i+1}"
    }
  },
  "atac.macs2_signal_track_pooled": {
    "pval_bw": {
      "path": "signal/pooled-rep/${basename}",
      "table": "Signal/Pooled replicate/MACS2 signal track (p-val)",
      "ucsc_track": "track type=bigWig name=\"MACS2 p-val (pooled)\" priority=0 smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"BW\np-val\"]",
      "subgraph": "cluster_pooled_rep"
    },
    "fc_bw": {
      "path": "signal/pooled-rep/${basename}",
      "table": "Signal/Pooled replicate/MACS2 signal track (fold-enrichment)",
      "ucsc_track": "track type=bigWig name=\"MACS2 fc (pooled)\" priority=0 smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"BW\nFC\"]",
      "subgraph": "cluster_pooled_rep"
    }
  },
  "atac.count_signal_track": {
    "pos_bw": {
      "path": "signal/rep${i+1}/${basename}",
      "table": "Signal/Replicate ${i+1}/Count signal track (positive)",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Count +\nSignal\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "neg_bw": {
      "path": "signal/rep${i+1}/${basename}",
      "table": "Signal/Replicate ${i+1}/Count signal track (negative)",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Count -\nSignal\"]",
      "subgraph": "cluster_pooled_rep"
    }
  },
  "atac.count_signal_track_pooled": {
    "pos_bw": {
      "path": "signal/pooled-rep/${basename}",
      "table": "Signal/Pooled replicate/Count signal track (positive)",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Count +\nSignal\"]",
      "subgraph": "cluster_rep${i+1}"
    },
    "neg_bw": {
      "path": "signal/pooled-rep/${basename}",
      "table": "Signal/Pooled replicate/Count signal track (negative)",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Count -\nSignal\"]",
      "subgraph": "cluster_pooled_rep"
    }
  },
  "atac.idr": {
    "bfilt_idr_peak": {
      "path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
      "table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak",
      "node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"IDR NPeak\n${basename.split('.')[0]}\"]"
    },
    "bfilt_idr_peak_bb": {
      "path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
      "table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak (BigBed)"
    },
    "bfilt_idr_peak_hammock": {
      "path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
      "table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Blacklist-filtered IDR peak (hammock)"
    },
    "idr_unthresholded_peak": {
      "path": "peak/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
      "table": "Peak/${basename.split('.')[0].replace('_vs_','_').replace('_',' vs. ').replace('-',' vs. ').capitalize()}/Unthresholded raw IDR peak"
    },
    "idr_plot": {
      "path": "qc/${basename.split('.')[0].replace('_vs_','_').replace('_','_vs_').replace('-','_vs_')}/${basename}",
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    "subgraph cluster_rep8":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 8\""},
    "subgraph cluster_rep9":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 9\""},
    "subgraph cluster_rep10": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 10\""},
    "subgraph cluster_pooled_ctl":{"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "oldlace", "labeljust": "\"l\"", "label": "\"Pooled control\""},
    "subgraph cluster_ctl1":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 1\""},
    "subgraph cluster_ctl2":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 2\""},
    "subgraph cluster_ctl3":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 3\""},
    "subgraph cluster_ctl4":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 4\""},
    "subgraph cluster_ctl5":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 5\""},
    "subgraph cluster_ctl6":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 6\""},
    "subgraph cluster_ctl7":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 7\""},
    "subgraph cluster_ctl8":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 8\""},
    "subgraph cluster_ctl9":  {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 9\""},
    "subgraph cluster_ctl10": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "darkgrey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Control 10\""}
  }
}