croo_out_def.json

{
  "hic.align": {
    "bam": {
      "path": "align/rep${i+1}/read_pair_${j+1}/${basename}",
      "table": "Align/Replicate ${i+1}/Read Pair ${j+1}/Raw BAM"
    }
  },
  "hic.arrowhead": {
    "out_file": {
      "path": "arrowhead/${basename}",
      "table": "Arrowhead TAD Calls"
    }
  },
  "hic.calculate_stats": {
    "stats": {
      "path": "calculate_stats/${basename}",
      "table": "Calculate Stats/Stats txt/MAPQ ${basename.split('.')[0].lstrip('stats_')}"
    },
    "stats_json": {
      "path": "calculate_stats/${basename}",
      "table": "Calculate Stats/Stats JSON/MAPQ ${basename.split('.')[0].lstrip('stats_')}"
    }
  },
  "hic.create_hic": {
    "output_hic": {
      "path": "create_hic/${basename}",
      "table": "Create HiC/HiC Files/MAPQ ${basename.split('.')[0].lstrip('inter_')}"
    }
  },
  "hic.dedup": {
    "deduped_bam": {
      "path": "dedup/rep${i+1}/${basename}",
      "table": "Filtering/Replicate ${i+1}/Filtered Merged BAMs"
    }
  },
  "hic.hiccups": {
    "out_file": {
      "path": "hiccups/${basename}",
      "table": "Hiccups Loop Calls"
    }
  }
}