{
 "placeholder": "<out>",
 "chromosomix": "0.19.0 at 997e59c",
 "threads": 4,
 "commands": [
  {
   "name": "insulation",
   "section": 1,
   "analysis": "Diamond insulation",
   "data": "mouse Hi-C, 10 kb, window 100 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "insulation",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--window",
    "10"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix insulation data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --window 10 --out insulation/app"
  },
  {
   "name": "cooltools-insulation",
   "section": 1,
   "analysis": "Diamond insulation",
   "data": "mouse Hi-C, 10 kb, window 100 kb",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "",
   "group": "",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_insulation.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>",
    "4"
   ],
   "out": "cooltools.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_insulation.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 insulation/cooltools.tsv 4"
  },
  {
   "name": "di",
   "section": 2,
   "analysis": "Directionality index",
   "data": "mouse Hi-C, 50 kb, window 2 Mb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "di",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/50000",
    "--window",
    "40"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix di data/4DNFIOZ1TRUS.mcool::/resolutions/50000 --window 40 --out di/app"
  },
  {
   "name": "domaincaller-di",
   "section": 2,
   "analysis": "Directionality index",
   "data": "mouse Hi-C, 50 kb, window 2 Mb",
   "tool": "domaincaller",
   "version": "0.1.0",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/domaincaller_di.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/50000",
    "<out>"
   ],
   "out": "domaincaller.npy",
   "env": null,
   "command": "python ../../scripts/domaincaller_di.py data/4DNFIOZ1TRUS.mcool::/resolutions/50000 di/domaincaller.npy"
  },
  {
   "name": "compartments",
   "section": 3,
   "analysis": "Compartments",
   "data": "mouse Hi-C, 100 kb, GC-phased",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "compartments",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "--components",
    "3",
    "--phaseTrack",
    "compartments/gc.bedGraph"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix compartments data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --components 3 --phaseTrack compartments/gc.bedGraph --out compartments/app"
  },
  {
   "name": "cooltools-eigs",
   "section": 3,
   "analysis": "Compartments",
   "data": "mouse Hi-C, 100 kb, GC-phased",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_eigs_cis.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "compartments/gc.tsv",
    "<out>"
   ],
   "out": "cooltools",
   "env": null,
   "command": "python ../../scripts/cooltools_eigs_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 compartments/gc.tsv compartments/cooltools"
  },
  {
   "name": "expected-yeast",
   "section": 4,
   "analysis": "P(s)",
   "data": "yeast Micro-C 800 bp; mouse Hi-C 10 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "yeast 800 bp",
   "group": "yeast 800 bp",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "expected",
    "data/GSE151553_A364_merged.mcool::/resolutions/800",
    "--quantity",
    "expected",
    "--scope",
    "file"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix expected data/GSE151553_A364_merged.mcool::/resolutions/800 --quantity expected --scope file --out ps/yeast"
  },
  {
   "name": "expected-mouse",
   "section": 4,
   "analysis": "P(s)",
   "data": "yeast Micro-C 800 bp; mouse Hi-C 10 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "mouse 10 kb",
   "group": "mouse 10 kb",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "expected",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--quantity",
    "expected",
    "--scope",
    "file"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix expected data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --quantity expected --scope file --out ps/mouse"
  },
  {
   "name": "cooltools-expected-yeast",
   "section": 4,
   "analysis": "P(s)",
   "data": "yeast Micro-C 800 bp; mouse Hi-C 10 kb",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "yeast 800 bp",
   "group": "yeast 800 bp",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_expected_cis.py",
    "data/GSE151553_A364_merged.mcool::/resolutions/800",
    "<out>",
    "4"
   ],
   "out": "yeast-cooltools.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_expected_cis.py data/GSE151553_A364_merged.mcool::/resolutions/800 ps/yeast-cooltools.tsv 4"
  },
  {
   "name": "cooltools-expected-mouse",
   "section": 4,
   "analysis": "P(s)",
   "data": "yeast Micro-C 800 bp; mouse Hi-C 10 kb",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "mouse 10 kb",
   "group": "mouse 10 kb",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_expected_cis.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>",
    "4"
   ],
   "out": "mouse-cooltools.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_expected_cis.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 ps/mouse-cooltools.tsv 4"
  },
  {
   "name": "peaks",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "peaks",
    "--signal",
    "data/4DNFIIY4QW2D.chr19.bw",
    "--replicate",
    "data/4DNFITBRHVZE.chr19.bw",
    "--perPeak",
    "--width",
    "150",
    "--times",
    "3",
    "--minWidth",
    "75",
    "--truncate",
    "100000",
    "--idr",
    "0.05"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix peaks --signal data/4DNFIIY4QW2D.chr19.bw --replicate data/4DNFITBRHVZE.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out yapc/app"
  },
  {
   "name": "yapc-seed0",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "seed 0",
   "group": "seed 0",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "0",
    "<out>",
    "cond",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 0 yapc/seed0/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "yapc-seed1",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "seed 1",
   "group": "seed 1",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "1",
    "<out>",
    "cond",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 1 yapc/seed1/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "yapc-seed2",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "seed 2",
   "group": "seed 2",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "2",
    "<out>",
    "cond",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 2 yapc/seed2/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "yapc-seed3",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "seed 3",
   "group": "seed 3",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "3",
    "<out>",
    "cond",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 3 yapc/seed3/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "yapc-seed4",
   "section": 5,
   "analysis": "Peak calling (yapc, IDR)",
   "data": "mouse ATAC-seq, 2 replicates, chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "seed 4",
   "group": "seed 4",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "4",
    "<out>",
    "cond",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 4 yapc/seed4/yapc cond data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "chromosight",
   "section": 6,
   "analysis": "Loops (chromosight)",
   "data": "yeast Micro-C, 800 bp",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "chromosight",
    "data/GSE151553_A364_merged.mcool::/resolutions/800",
    "--pattern",
    "loops"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix chromosight data/GSE151553_A364_merged.mcool::/resolutions/800 --pattern loops --out loops/app"
  },
  {
   "name": "chromosight",
   "section": 6,
   "analysis": "Loops (chromosight)",
   "data": "yeast Micro-C, 800 bp",
   "tool": "chromosight",
   "version": "1.6.3",
   "variant": "",
   "group": "",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/chromosight",
    "detect",
    "--pattern",
    "loops",
    "--threads",
    "4",
    "data/GSE151553_A364_merged.mcool::/resolutions/800",
    "<out>"
   ],
   "out": "loops",
   "env": null,
   "command": "chromosight detect --pattern loops --threads 4 data/GSE151553_A364_merged.mcool::/resolutions/800 loops/chromosight/loops"
  },
  {
   "name": "hicrep",
   "section": 7,
   "analysis": "Reproducibility (HiCRep)",
   "data": "chicken Hi-C, 3 maps, 100 kb, raw counts",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "3 maps, 3 pairs",
   "group": "3 maps, 3 pairs",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "hicrep",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "--against",
    "data/4DNFITBCUX56.mcool::/resolutions/100000",
    "--against",
    "data/4DNFIIML46E5.mcool::/resolutions/100000",
    "--maxDistance",
    "50",
    "--smooth",
    "1",
    "--no-balance",
    "--sequences",
    "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix hicrep data/4DNFIH8L6WON.mcool::/resolutions/100000 --against data/4DNFITBCUX56.mcool::/resolutions/100000 --against data/4DNFIIML46E5.mcool::/resolutions/100000 --maxDistance 50 --smooth 1 --no-balance --sequences chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ --out hicrep/app"
  },
  {
   "name": "hicrep",
   "section": 7,
   "analysis": "Reproducibility (HiCRep)",
   "data": "chicken Hi-C, 3 maps, 100 kb, raw counts",
   "tool": "hicrep",
   "version": "0.2.6",
   "variant": "3 maps, 3 pairs",
   "group": "3 maps, 3 pairs",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/hicrep_scc.py",
    "<out>",
    "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ",
    "4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000",
    "4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000"
   ],
   "out": "hicrep.tsv",
   "env": null,
   "command": "python ../../scripts/hicrep_scc.py hicrep/hicrep.tsv chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr17,chr18,chr19,chr20,chr21,chr23,chr24,chr26,chr27,chrW,chrZ 4DNFIH8L6WON=data/4DNFIH8L6WON.mcool::/resolutions/100000 4DNFITBCUX56=data/4DNFITBCUX56.mcool::/resolutions/100000 4DNFIIML46E5=data/4DNFIIML46E5.mcool::/resolutions/100000"
  },
  {
   "name": "reconstruct3d-seed0",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "seed 0",
   "group": "seed 0",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "reconstruct3d",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "--method",
    "nb",
    "--alpha",
    "3",
    "--seed",
    "0"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 0 --out pastis/app-seed0"
  },
  {
   "name": "reconstruct3d-seed1",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "seed 1",
   "group": "seed 1",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "reconstruct3d",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "--method",
    "nb",
    "--alpha",
    "3",
    "--seed",
    "1"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 1 --out pastis/app-seed1"
  },
  {
   "name": "reconstruct3d-seed2",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "seed 2",
   "group": "seed 2",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "reconstruct3d",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "--method",
    "nb",
    "--alpha",
    "3",
    "--seed",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix reconstruct3d data/GSE151553_A364_merged.mcool::/resolutions/12800 --method nb --alpha 3 --seed 2 --out pastis/app-seed2"
  },
  {
   "name": "pastis-seed0",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "pastis",
   "version": "0.5.0",
   "variant": "seed 0",
   "group": "seed 0",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pastis_nb.py",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "<out>",
    "0"
   ],
   "out": "pastis-seed0.npy",
   "env": null,
   "command": "python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed0.npy 0"
  },
  {
   "name": "pastis-seed1",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "pastis",
   "version": "0.5.0",
   "variant": "seed 1",
   "group": "seed 1",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pastis_nb.py",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "<out>",
    "1"
   ],
   "out": "pastis-seed1.npy",
   "env": null,
   "command": "python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed1.npy 1"
  },
  {
   "name": "pastis-seed2",
   "section": 8,
   "analysis": "3D model (pastis-NB)",
   "data": "yeast Micro-C, 12.8 kb, 905 beads",
   "tool": "pastis",
   "version": "0.5.0",
   "variant": "seed 2",
   "group": "seed 2",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pastis_nb.py",
    "data/GSE151553_A364_merged.mcool::/resolutions/12800",
    "<out>",
    "2"
   ],
   "out": "pastis-seed2.npy",
   "env": null,
   "command": "python ../../scripts/pastis_nb.py data/GSE151553_A364_merged.mcool::/resolutions/12800 pastis/pastis-seed2.npy 2"
  },
  {
   "name": "coverage-raw",
   "section": 9,
   "analysis": "Coverage",
   "data": "mouse Hi-C, 10 kb, raw and balanced",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "raw",
   "group": "raw",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "coverage",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--cis",
    "--trans",
    "--fraction"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --out coverage/raw"
  },
  {
   "name": "coverage-balanced",
   "section": 9,
   "analysis": "Coverage",
   "data": "mouse Hi-C, 10 kb, raw and balanced",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "balanced",
   "group": "balanced",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "coverage",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--cis",
    "--trans",
    "--fraction",
    "--balance"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix coverage data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --cis --trans --fraction --balance --out coverage/balanced"
  },
  {
   "name": "cooltools-coverage-raw",
   "section": 9,
   "analysis": "Coverage",
   "data": "mouse Hi-C, 10 kb, raw and balanced",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "raw",
   "group": "raw",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_coverage.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>",
    "4"
   ],
   "out": "cooltools-raw.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-raw.tsv 4"
  },
  {
   "name": "cooltools-coverage-balanced",
   "section": 9,
   "analysis": "Coverage",
   "data": "mouse Hi-C, 10 kb, raw and balanced",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "balanced",
   "group": "balanced",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_coverage.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>",
    "4",
    "weight"
   ],
   "out": "cooltools-balanced.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_coverage.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 coverage/cooltools-balanced.tsv 4 weight"
  },
  {
   "name": "fourc-Sox2",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "Sox2",
   "group": "Sox2",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "fourc",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--anchor",
    "chr3:34,650,001-34,660,000",
    "--no-cis"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr3:34,650,001-34,660,000 --no-cis --out virtual4c/Sox2"
  },
  {
   "name": "fourc-Nanog",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "Nanog",
   "group": "Nanog",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "fourc",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--anchor",
    "chr6:122,700,001-122,710,000",
    "--no-cis"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr6:122,700,001-122,710,000 --no-cis --out virtual4c/Nanog"
  },
  {
   "name": "fourc-Pou5f1",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "Pou5f1",
   "group": "Pou5f1",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "fourc",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--anchor",
    "chr17:35,500,001-35,510,000",
    "--no-cis"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix fourc data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchor chr17:35,500,001-35,510,000 --no-cis --out virtual4c/Pou5f1"
  },
  {
   "name": "cooltools-virtual4c-Sox2",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "Sox2",
   "group": "Sox2",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_virtual4c.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "chr3:34650000-34660000",
    "<out>",
    "4"
   ],
   "out": "cooltools-Sox2.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr3:34650000-34660000 virtual4c/cooltools-Sox2.tsv 4"
  },
  {
   "name": "cooltools-virtual4c-Nanog",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "Nanog",
   "group": "Nanog",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_virtual4c.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "chr6:122700000-122710000",
    "<out>",
    "4"
   ],
   "out": "cooltools-Nanog.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr6:122700000-122710000 virtual4c/cooltools-Nanog.tsv 4"
  },
  {
   "name": "cooltools-virtual4c-Pou5f1",
   "section": 10,
   "analysis": "Virtual 4C",
   "data": "mouse Hi-C, 10 kb, three viewpoints, whole genome",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "Pou5f1",
   "group": "Pou5f1",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_virtual4c.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "chr17:35500000-35510000",
    "<out>",
    "4"
   ],
   "out": "cooltools-Pou5f1.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_virtual4c.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chr17:35500000-35510000 virtual4c/cooltools-Pou5f1.tsv 4"
  },
  {
   "name": "apa-raw",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "raw",
   "group": "raw",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "none",
    "--minDist",
    "12",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/raw"
  },
  {
   "name": "apa-oe",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "over the expected",
   "group": "over the expected",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "oe",
    "--minDist",
    "12",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm oe --minDist 12 --mode fixed --window 5 --minDiag 2 --out apa/oe"
  },
  {
   "name": "apa-raw-every",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "raw, every loop",
   "group": "raw, every loop",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "none",
    "--minDist",
    "0",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/raw-every"
  },
  {
   "name": "apa-oe-every",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "over the expected, every loop",
   "group": "over the expected, every loop",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "oe",
    "--minDist",
    "0",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm oe --minDist 0 --mode fixed --window 5 --minDiag 2 --out apa/oe-every"
  },
  {
   "name": "apa-local",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "on the diagonal, raw",
   "group": "on the diagonal, raw",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--anchors",
    "features",
    "--features",
    "apa/anchors.bed",
    "--norm",
    "none",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm none --mode fixed --window 5 --minDiag 2 --out apa/local"
  },
  {
   "name": "apa-local-oe",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "on the diagonal, over the expected",
   "group": "on the diagonal, over the expected",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--anchors",
    "features",
    "--features",
    "apa/anchors.bed",
    "--norm",
    "oe",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --anchors features --features apa/anchors.bed --norm oe --mode fixed --window 5 --minDiag 2 --out apa/local-oe"
  },
  {
   "name": "apa-controls-seed1",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "controls, seed 1",
   "group": "controls",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "matched",
    "--controls",
    "5",
    "--minShift",
    "50",
    "--maxShift",
    "500",
    "--seed",
    "1",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2",
    "--minDist",
    "12"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 1 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed1"
  },
  {
   "name": "apa-controls-seed2",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "controls, seed 2",
   "group": "controls",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "matched",
    "--controls",
    "5",
    "--minShift",
    "50",
    "--maxShift",
    "500",
    "--seed",
    "2",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2",
    "--minDist",
    "12"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 2 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed2"
  },
  {
   "name": "apa-controls-seed3",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "controls, seed 3",
   "group": "controls",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "matched",
    "--controls",
    "5",
    "--minShift",
    "50",
    "--maxShift",
    "500",
    "--seed",
    "3",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2",
    "--minDist",
    "12"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 3 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed3"
  },
  {
   "name": "apa-controls-seed4",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "controls, seed 4",
   "group": "controls",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "matched",
    "--controls",
    "5",
    "--minShift",
    "50",
    "--maxShift",
    "500",
    "--seed",
    "4",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2",
    "--minDist",
    "12"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 4 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed4"
  },
  {
   "name": "apa-controls-seed5",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "controls, seed 5",
   "group": "controls",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "matched",
    "--controls",
    "5",
    "--minShift",
    "50",
    "--maxShift",
    "500",
    "--seed",
    "5",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2",
    "--minDist",
    "12"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm matched --controls 5 --minShift 50 --maxShift 500 --seed 5 --mode fixed --window 5 --minDiag 2 --minDist 12 --out apa/controls-seed5"
  },
  {
   "name": "chromosight-mouse",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosight",
   "version": "1.6.3",
   "variant": "the loops, called",
   "group": "the loops, called",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/chromosight",
    "detect",
    "--pattern",
    "loops",
    "--threads",
    "4",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>"
   ],
   "out": "loops",
   "env": null,
   "command": "chromosight detect --pattern loops --threads 4 data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops"
  },
  {
   "name": "coolpuppy-raw",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "raw",
   "group": "raw",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4"
   ],
   "out": "coolpuppy-raw.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw.tsv 4"
  },
  {
   "name": "coolpuppy-oe",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "over the expected",
   "group": "over the expected",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--expected",
    "ps/mouse-cooltools.tsv"
   ],
   "out": "coolpuppy-oe.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-oe.tsv 4 --expected ps/mouse-cooltools.tsv"
  },
  {
   "name": "coolpuppy-raw-every",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "raw, every loop",
   "group": "raw, every loop",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--mindist",
    "0"
   ],
   "out": "coolpuppy-raw-every.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-raw-every.tsv 4 --mindist 0"
  },
  {
   "name": "coolpuppy-oe-every",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "over the expected, every loop",
   "group": "over the expected, every loop",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--expected",
    "ps/mouse-cooltools.tsv",
    "--mindist",
    "0"
   ],
   "out": "coolpuppy-oe-every.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-oe-every.tsv 4 --expected ps/mouse-cooltools.tsv --mindist 0"
  },
  {
   "name": "coolpuppy-local",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "on the diagonal, raw",
   "group": "on the diagonal, raw",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/anchors.bed",
    "50000",
    "<out>",
    "4",
    "--local"
   ],
   "out": "coolpuppy-local.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local.tsv 4 --local"
  },
  {
   "name": "coolpuppy-local-oe",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "on the diagonal, over the expected",
   "group": "on the diagonal, over the expected",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/anchors.bed",
    "50000",
    "<out>",
    "4",
    "--local",
    "--expected",
    "ps/mouse-cooltools.tsv"
   ],
   "out": "coolpuppy-local-oe.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/anchors.bed 50000 apa/coolpuppy-local-oe.tsv 4 --local --expected ps/mouse-cooltools.tsv"
  },
  {
   "name": "coolpuppy-controls-seed0",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "controls, seed 0",
   "group": "controls",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--nshifts",
    "5",
    "--minshift",
    "500000",
    "--maxshift",
    "5005000",
    "--seed",
    "0"
   ],
   "out": "coolpuppy-controls-seed0.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed0.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 0"
  },
  {
   "name": "coolpuppy-controls-seed1",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "controls, seed 1",
   "group": "controls",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--nshifts",
    "5",
    "--minshift",
    "500000",
    "--maxshift",
    "5005000",
    "--seed",
    "1"
   ],
   "out": "coolpuppy-controls-seed1.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed1.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 1"
  },
  {
   "name": "coolpuppy-controls-seed2",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "controls, seed 2",
   "group": "controls",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--nshifts",
    "5",
    "--minshift",
    "500000",
    "--maxshift",
    "5005000",
    "--seed",
    "2"
   ],
   "out": "coolpuppy-controls-seed2.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed2.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 2"
  },
  {
   "name": "coolpuppy-controls-seed3",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "controls, seed 3",
   "group": "controls",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--nshifts",
    "5",
    "--minshift",
    "500000",
    "--maxshift",
    "5005000",
    "--seed",
    "3"
   ],
   "out": "coolpuppy-controls-seed3.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed3.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 3"
  },
  {
   "name": "coolpuppy-controls-seed4",
   "section": 11,
   "analysis": "Aggregate peak analysis",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "controls, seed 4",
   "group": "controls",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "apa/loops.bedpe",
    "50000",
    "<out>",
    "4",
    "--nshifts",
    "5",
    "--minshift",
    "500000",
    "--maxshift",
    "5005000",
    "--seed",
    "4"
   ],
   "out": "coolpuppy-controls-seed4.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 apa/loops.bedpe 50000 apa/coolpuppy-controls-seed4.tsv 4 --nshifts 5 --minshift 500000 --maxshift 5005000 --seed 4"
  },
  {
   "name": "apa-chromosight",
   "section": 12,
   "analysis": "APA, chromosight's score",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "--pairs",
    "apa/loops.bedpe",
    "--norm",
    "chromosight"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --pairs apa/loops.bedpe --norm chromosight --out chromosight-quantify/app"
  },
  {
   "name": "chromosight-quantify",
   "section": 12,
   "analysis": "APA, chromosight's score",
   "data": "mouse Hi-C, 10 kb, 2,515 loops",
   "tool": "chromosight",
   "version": "1.6.3",
   "variant": "",
   "group": "",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/chromosight",
    "quantify",
    "--pattern",
    "loops",
    "--threads",
    "4",
    "apa/loops.bedpe",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>"
   ],
   "out": "quantify",
   "env": null,
   "command": "chromosight quantify --pattern loops --threads 4 apa/loops.bedpe data/4DNFIOZ1TRUS.mcool::/resolutions/10000 chromosight-quantify/quantify"
  },
  {
   "name": "boost-chr19",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "chr19, 615 bins",
   "group": "chr19, 615 bins",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "boost",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "--sequences",
    "chr19"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr19 --out boost-hic/chr19"
  },
  {
   "name": "boost-chr11",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "chr11, 1,221 bins",
   "group": "chr11, 1,221 bins",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "boost",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "--sequences",
    "chr11"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr11 --out boost-hic/chr11"
  },
  {
   "name": "boost-chr1",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "chr1, 1,955 bins",
   "group": "chr1, 1,955 bins",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "boost",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "--sequences",
    "chr1"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix boost data/4DNFIOZ1TRUS.mcool::/resolutions/100000 --sequences chr1 --out boost-hic/chr1"
  },
  {
   "name": "boosthic-chr19",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "Boost-HiC",
   "version": "a615aff",
   "variant": "chr19, 615 bins",
   "group": "chr19, 615 bins",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/boosthic.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "chr19",
    "<out>"
   ],
   "out": "boosthic-chr19",
   "env": {
    "BOOSTHIC_DIR": "/home/runner/work/_temp/Boost-HiC"
   },
   "command": "python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr19 boost-hic/boosthic-chr19"
  },
  {
   "name": "boosthic-chr11",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "Boost-HiC",
   "version": "a615aff",
   "variant": "chr11, 1,221 bins",
   "group": "chr11, 1,221 bins",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/boosthic.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "chr11",
    "<out>"
   ],
   "out": "boosthic-chr11",
   "env": {
    "BOOSTHIC_DIR": "/home/runner/work/_temp/Boost-HiC"
   },
   "command": "python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr11 boost-hic/boosthic-chr11"
  },
  {
   "name": "boosthic-chr1",
   "section": 13,
   "analysis": "Boost-HiC",
   "data": "mouse Hi-C, 100 kb, chr19, chr11, chr1",
   "tool": "Boost-HiC",
   "version": "a615aff",
   "variant": "chr1, 1,955 bins",
   "group": "chr1, 1,955 bins",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/boosthic.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "chr1",
    "<out>"
   ],
   "out": "boosthic-chr1",
   "env": {
    "BOOSTHIC_DIR": "/home/runner/work/_temp/Boost-HiC"
   },
   "command": "python ../../scripts/boosthic.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 chr1 boost-hic/boosthic-chr1"
  },
  {
   "name": "metaplot",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "TSS",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "metaplot",
    "--tracks",
    "data/4DNFIIY4QW2D.bw",
    "--features",
    "metaplot/transcripts.bed",
    "--mode",
    "reference",
    "--at",
    "start",
    "--flank",
    "2000",
    "--step",
    "50",
    "--band",
    "none"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app"
  },
  {
   "name": "metaplot-two",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "TSS, two tracks",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "metaplot",
    "--tracks",
    "data/4DNFIIY4QW2D.bw",
    "--tracks",
    "data/4DNFITBRHVZE.bw",
    "--features",
    "metaplot/transcripts.bed",
    "--mode",
    "reference",
    "--at",
    "start",
    "--flank",
    "2000",
    "--step",
    "50",
    "--band",
    "none"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix metaplot --tracks data/4DNFIIY4QW2D.bw --tracks data/4DNFITBRHVZE.bw --features metaplot/transcripts.bed --mode reference --at start --flank 2000 --step 50 --band none --out metaplot/app-two"
  },
  {
   "name": "computematrix",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "computeMatrix",
   "group": "TSS",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/computeMatrix",
    "reference-point",
    "-S",
    "data/4DNFIIY4QW2D.bw",
    "-R",
    "metaplot/transcripts.bed",
    "--referencePoint",
    "TSS",
    "-b",
    "2000",
    "-a",
    "2000",
    "--binSize",
    "50",
    "-p",
    "4",
    "-o",
    "<out>"
   ],
   "out": "deeptools.mat.gz",
   "env": null,
   "command": "computeMatrix reference-point -S data/4DNFIIY4QW2D.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools.mat.gz"
  },
  {
   "name": "plotprofile",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotProfile",
   "group": "TSS",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotProfile",
    "-m",
    "metaplot/deeptools.mat.gz",
    "-out",
    "<out>.png",
    "--outFileNameData",
    "<out>.tab"
   ],
   "out": "deeptools-profile",
   "env": null,
   "command": "plotProfile -m metaplot/deeptools.mat.gz -out metaplot/deeptools-profile.png --outFileNameData metaplot/deeptools-profile.tab"
  },
  {
   "name": "computematrix-two",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "computeMatrix",
   "group": "TSS, two tracks",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/computeMatrix",
    "reference-point",
    "-S",
    "data/4DNFIIY4QW2D.bw",
    "data/4DNFITBRHVZE.bw",
    "-R",
    "metaplot/transcripts.bed",
    "--referencePoint",
    "TSS",
    "-b",
    "2000",
    "-a",
    "2000",
    "--binSize",
    "50",
    "-p",
    "4",
    "-o",
    "<out>"
   ],
   "out": "deeptools-two.mat.gz",
   "env": null,
   "command": "computeMatrix reference-point -S data/4DNFIIY4QW2D.bw data/4DNFITBRHVZE.bw -R metaplot/transcripts.bed --referencePoint TSS -b 2000 -a 2000 --binSize 50 -p 4 -o metaplot/deeptools-two.mat.gz"
  },
  {
   "name": "plotprofile-two",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotProfile",
   "group": "TSS, two tracks",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotProfile",
    "-m",
    "metaplot/deeptools-two.mat.gz",
    "-out",
    "<out>.png",
    "--outFileNameData",
    "<out>.tab"
   ],
   "out": "deeptools-two-profile",
   "env": null,
   "command": "plotProfile -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-profile.png --outFileNameData metaplot/deeptools-two-profile.tab"
  },
  {
   "name": "plotheatmap-two",
   "section": 14,
   "analysis": "Metaplot",
   "data": "mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotHeatmap",
   "group": "TSS, two tracks",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotHeatmap",
    "-m",
    "metaplot/deeptools-two.mat.gz",
    "-out",
    "<out>.png",
    "--outFileSortedRegions",
    "<out>.bed"
   ],
   "out": "deeptools-two-heatmap",
   "env": null,
   "command": "plotHeatmap -m metaplot/deeptools-two.mat.gz -out metaplot/deeptools-two-heatmap.png --outFileSortedRegions metaplot/deeptools-two-heatmap.bed"
  },
  {
   "name": "overlap",
   "section": 15,
   "analysis": "Interval overlap",
   "data": "ATAC-seq peaks (§ 5) and promoters, chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "overlap",
    "--sequence",
    "data/mm10.fa",
    "--features",
    "yapc/seed0/yapc_0.05.bed",
    "--features",
    "overlap/promoters.bed",
    "--a",
    "yapc/seed0/yapc_0.05.bed",
    "--b",
    "overlap/promoters.bed",
    "--shuffle",
    "--iterations",
    "1000",
    "--seed",
    "1"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix overlap --sequence data/mm10.fa --features yapc/seed0/yapc_0.05.bed --features overlap/promoters.bed --a yapc/seed0/yapc_0.05.bed --b overlap/promoters.bed --shuffle --iterations 1000 --seed 1 --out overlap/app"
  },
  {
   "name": "bedtools-overlap",
   "section": 15,
   "analysis": "Interval overlap",
   "data": "ATAC-seq peaks (§ 5) and promoters, chr19",
   "tool": "bedtools",
   "version": "2.31.1",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/bedtools_overlap.py",
    "yapc/seed0/yapc_0.05.bed",
    "overlap/promoters.bed",
    "overlap/mm10.genome",
    "1000",
    "<out>"
   ],
   "out": "bedtools",
   "env": null,
   "command": "python ../../scripts/bedtools_overlap.py yapc/seed0/yapc_0.05.bed overlap/promoters.bed overlap/mm10.genome 1000 overlap/bedtools"
  },
  {
   "name": "composition",
   "section": 16,
   "analysis": "Base composition",
   "data": "mm10, 10 kb bins",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "composition",
    "--sequence",
    "data/mm10.fa",
    "--resolution",
    "10000"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix composition --sequence data/mm10.fa --resolution 10000 --out composition/app"
  },
  {
   "name": "composition",
   "section": 16,
   "analysis": "Base composition",
   "data": "mm10, 10 kb bins",
   "tool": "bioframe, Biopython",
   "version": "0.8.0, 1.88",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/composition.py",
    "data/mm10.fa",
    "10000",
    "<out>"
   ],
   "out": "reference.tsv",
   "env": null,
   "command": "python ../../scripts/composition.py data/mm10.fa 10000 composition/reference.tsv"
  },
  {
   "name": "motif-TGACTCA",
   "section": 17,
   "analysis": "Motif search",
   "data": "mm10 chr19, two motifs, both strands",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "TGACTCA, ≤ 1 mismatch",
   "group": "TGACTCA, ≤ 1 mismatch",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "motif",
    "--sequence",
    "data/mm10.chr19.fa",
    "--pattern",
    "TGACTCA",
    "--mismatches",
    "1"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix motif --sequence data/mm10.chr19.fa --pattern TGACTCA --mismatches 1 --out motif/TGACTCA"
  },
  {
   "name": "motif-WGATAR",
   "section": 17,
   "analysis": "Motif search",
   "data": "mm10 chr19, two motifs, both strands",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "WGATAR",
   "group": "WGATAR",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "motif",
    "--sequence",
    "data/mm10.chr19.fa",
    "--pattern",
    "WGATAR",
    "--mismatches",
    "0"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix motif --sequence data/mm10.chr19.fa --pattern WGATAR --mismatches 0 --out motif/WGATAR"
  },
  {
   "name": "seqkit-TGACTCA",
   "section": 17,
   "analysis": "Motif search",
   "data": "mm10 chr19, two motifs, both strands",
   "tool": "seqkit",
   "version": "2.3.0",
   "variant": "TGACTCA, ≤ 1 mismatch",
   "group": "TGACTCA, ≤ 1 mismatch",
   "threads": 4,
   "bench": true,
   "argv": [
    "/usr/bin/seqkit",
    "locate",
    "-i",
    "-m",
    "1",
    "-p",
    "TGACTCA",
    "--bed",
    "-j",
    "4",
    "data/mm10.chr19.fa",
    "-o",
    "<out>"
   ],
   "out": "seqkit-TGACTCA.bed",
   "env": null,
   "command": "seqkit locate -i -m 1 -p TGACTCA --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-TGACTCA.bed"
  },
  {
   "name": "seqkit-WGATAR",
   "section": 17,
   "analysis": "Motif search",
   "data": "mm10 chr19, two motifs, both strands",
   "tool": "seqkit",
   "version": "2.3.0",
   "variant": "WGATAR",
   "group": "WGATAR",
   "threads": 4,
   "bench": true,
   "argv": [
    "/usr/bin/seqkit",
    "locate",
    "-i",
    "-d",
    "-p",
    "WGATAR",
    "--bed",
    "-j",
    "4",
    "data/mm10.chr19.fa",
    "-o",
    "<out>"
   ],
   "out": "seqkit-WGATAR.bed",
   "env": null,
   "command": "seqkit locate -i -d -p WGATAR --bed -j 4 data/mm10.chr19.fa -o motif/seqkit-WGATAR.bed"
  },
  {
   "name": "trackcorr-100-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "100 bp, pearson",
   "group": "100 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "100",
    "--method",
    "pearson"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method pearson --out trackcorr/app-100-pearson"
  },
  {
   "name": "trackcorr-100-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "100 bp, spearman",
   "group": "100 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "100",
    "--method",
    "spearman"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 100 --method spearman --out trackcorr/app-100-spearman"
  },
  {
   "name": "trackcorr-1000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "1,000 bp, pearson",
   "group": "1,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "1000",
    "--method",
    "pearson"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method pearson --out trackcorr/app-1000-pearson"
  },
  {
   "name": "trackcorr-1000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "1,000 bp, spearman",
   "group": "1,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "1000",
    "--method",
    "spearman"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 1000 --method spearman --out trackcorr/app-1000-spearman"
  },
  {
   "name": "trackcorr-10000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "10,000 bp, pearson",
   "group": "10,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "10000",
    "--method",
    "pearson"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method pearson --out trackcorr/app-10000-pearson"
  },
  {
   "name": "trackcorr-10000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "10,000 bp, spearman",
   "group": "10,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "trackcorr",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw",
    "--binsize",
    "10000",
    "--method",
    "spearman"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix trackcorr --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw,data/4DNFIUJ5CJVN.chr19.bw --binsize 10000 --method spearman --out trackcorr/app-10000-spearman"
  },
  {
   "name": "pybigwig-correlation-100-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "100 bp, pearson",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "100",
    "pearson",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-100-pearson.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-100-pearson.tsv 100 pearson data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "pybigwig-correlation-100-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "100 bp, spearman",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "100",
    "spearman",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-100-spearman.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-100-spearman.tsv 100 spearman data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "multibigwigsummary-100",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "100 bp, the windows",
   "group": "100 bp windows",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/multiBigwigSummary",
    "bins",
    "-b",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw",
    "--binSize",
    "100",
    "-p",
    "4",
    "-o",
    "<out>.npz",
    "--outRawCounts",
    "<out>.tab"
   ],
   "out": "deeptools-100",
   "env": null,
   "command": "multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 100 -p 4 -o trackcorr/deeptools-100.npz --outRawCounts trackcorr/deeptools-100.tab"
  },
  {
   "name": "plotcorrelation-100-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "100 bp, pearson",
   "group": "100 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-100.npz",
    "-c",
    "pearson",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-100-pearson",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-100.npz -c pearson -p heatmap -o trackcorr/deeptools-100-pearson.png --outFileCorMatrix trackcorr/deeptools-100-pearson.tab"
  },
  {
   "name": "plotcorrelation-100-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "100 bp, spearman",
   "group": "100 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-100.npz",
    "-c",
    "spearman",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-100-spearman",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-100.npz -c spearman -p heatmap -o trackcorr/deeptools-100-spearman.png --outFileCorMatrix trackcorr/deeptools-100-spearman.tab"
  },
  {
   "name": "pybigwig-correlation-1000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "1,000 bp, pearson",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "1000",
    "pearson",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-1000-pearson.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-1000-pearson.tsv 1000 pearson data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "pybigwig-correlation-1000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "1,000 bp, spearman",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "1000",
    "spearman",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-1000-spearman.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-1000-spearman.tsv 1000 spearman data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "multibigwigsummary-1000",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "1,000 bp, the windows",
   "group": "1,000 bp windows",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/multiBigwigSummary",
    "bins",
    "-b",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw",
    "--binSize",
    "1000",
    "-p",
    "4",
    "-o",
    "<out>.npz",
    "--outRawCounts",
    "<out>.tab"
   ],
   "out": "deeptools-1000",
   "env": null,
   "command": "multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 1000 -p 4 -o trackcorr/deeptools-1000.npz --outRawCounts trackcorr/deeptools-1000.tab"
  },
  {
   "name": "plotcorrelation-1000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "1,000 bp, pearson",
   "group": "1,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-1000.npz",
    "-c",
    "pearson",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-1000-pearson",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-1000.npz -c pearson -p heatmap -o trackcorr/deeptools-1000-pearson.png --outFileCorMatrix trackcorr/deeptools-1000-pearson.tab"
  },
  {
   "name": "plotcorrelation-1000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "1,000 bp, spearman",
   "group": "1,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-1000.npz",
    "-c",
    "spearman",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-1000-spearman",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-1000.npz -c spearman -p heatmap -o trackcorr/deeptools-1000-spearman.png --outFileCorMatrix trackcorr/deeptools-1000-spearman.tab"
  },
  {
   "name": "pybigwig-correlation-10000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "10,000 bp, pearson",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "10000",
    "pearson",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-10000-pearson.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-10000-pearson.tsv 10000 pearson data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "pybigwig-correlation-10000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "10,000 bp, spearman",
   "group": "exact means",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_correlation.py",
    "<out>",
    "10000",
    "spearman",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw"
   ],
   "out": "exact-10000-spearman.tsv",
   "env": null,
   "command": "python ../../scripts/pybigwig_correlation.py trackcorr/exact-10000-spearman.tsv 10000 spearman data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw"
  },
  {
   "name": "multibigwigsummary-10000",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "10,000 bp, the windows",
   "group": "10,000 bp windows",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/multiBigwigSummary",
    "bins",
    "-b",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw",
    "data/4DNFIUJ5CJVN.chr19.bw",
    "--binSize",
    "10000",
    "-p",
    "4",
    "-o",
    "<out>.npz",
    "--outRawCounts",
    "<out>.tab"
   ],
   "out": "deeptools-10000",
   "env": null,
   "command": "multiBigwigSummary bins -b data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw data/4DNFIUJ5CJVN.chr19.bw --binSize 10000 -p 4 -o trackcorr/deeptools-10000.npz --outRawCounts trackcorr/deeptools-10000.tab"
  },
  {
   "name": "plotcorrelation-10000-pearson",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "10,000 bp, pearson",
   "group": "10,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-10000.npz",
    "-c",
    "pearson",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-10000-pearson",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-10000.npz -c pearson -p heatmap -o trackcorr/deeptools-10000-pearson.png --outFileCorMatrix trackcorr/deeptools-10000-pearson.tab"
  },
  {
   "name": "plotcorrelation-10000-spearman",
   "section": 18,
   "analysis": "Track correlation",
   "data": "mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "10,000 bp, spearman",
   "group": "10,000 bp windows",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotCorrelation",
    "-in",
    "trackcorr/deeptools-10000.npz",
    "-c",
    "spearman",
    "-p",
    "heatmap",
    "-o",
    "<out>.png",
    "--outFileCorMatrix",
    "<out>.tab"
   ],
   "out": "deeptools-10000-spearman",
   "env": null,
   "command": "plotCorrelation -in trackcorr/deeptools-10000.npz -c spearman -p heatmap -o trackcorr/deeptools-10000-spearman.png --outFileCorMatrix trackcorr/deeptools-10000-spearman.tab"
  },
  {
   "name": "loops",
   "section": 19,
   "analysis": "Loop calling",
   "data": "mouse Hi-C, 10 kb, every chromosome",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "loops",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix loops data/4DNFIOZ1TRUS.mcool::/resolutions/10000 --out loopcalling/app"
  },
  {
   "name": "cooltools-dots",
   "section": 19,
   "analysis": "Loop calling",
   "data": "mouse Hi-C, 10 kb, every chromosome",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "",
   "group": "",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_dots.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/10000",
    "<out>",
    "4"
   ],
   "out": "cooltools.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_dots.py data/4DNFIOZ1TRUS.mcool::/resolutions/10000 loopcalling/cooltools.tsv 4"
  },
  {
   "name": "cistrans-raw",
   "section": 20,
   "analysis": "Cis and trans per sequence",
   "data": "chicken Hi-C, 100 kb, 36 sequences, raw and balanced",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "raw counts",
   "group": "raw counts",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "cistrans",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "--no-balance",
    "--normalise",
    "raw"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix cistrans data/4DNFIH8L6WON.mcool::/resolutions/100000 --no-balance --normalise raw --out cistrans/raw"
  },
  {
   "name": "cistrans-balanced",
   "section": 20,
   "analysis": "Cis and trans per sequence",
   "data": "chicken Hi-C, 100 kb, 36 sequences, raw and balanced",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "balanced",
   "group": "balanced",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "cistrans",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "--normalise",
    "raw"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix cistrans data/4DNFIH8L6WON.mcool::/resolutions/100000 --normalise raw --out cistrans/balanced"
  },
  {
   "name": "cistrans-indifference",
   "section": 20,
   "analysis": "Cis and trans per sequence",
   "data": "chicken Hi-C, 100 kb, 36 sequences, raw and balanced",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "balanced, against indifference",
   "group": "balanced, against indifference",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "cistrans",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix cistrans data/4DNFIH8L6WON.mcool::/resolutions/100000 --out cistrans/indifference"
  },
  {
   "name": "cooltools-cistrans-raw",
   "section": 20,
   "analysis": "Cis and trans per sequence",
   "data": "chicken Hi-C, 100 kb, 36 sequences, raw and balanced",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "raw",
   "group": "raw",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_cistrans.py",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "<out>",
    "4"
   ],
   "out": "cooltools-raw.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_cistrans.py data/4DNFIH8L6WON.mcool::/resolutions/100000 cistrans/cooltools-raw.tsv 4"
  },
  {
   "name": "cooltools-cistrans-balanced",
   "section": 20,
   "analysis": "Cis and trans per sequence",
   "data": "chicken Hi-C, 100 kb, 36 sequences, raw and balanced",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "balanced",
   "group": "balanced",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_cistrans.py",
    "data/4DNFIH8L6WON.mcool::/resolutions/100000",
    "<out>",
    "4",
    "weight"
   ],
   "out": "cooltools-balanced.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_cistrans.py data/4DNFIH8L6WON.mcool::/resolutions/100000 cistrans/cooltools-balanced.tsv 4 weight"
  },
  {
   "name": "cooltools-saddle",
   "section": 21,
   "analysis": "Saddle",
   "data": "mouse Hi-C, 100 kb, § 3's E1, 20 chromosomes",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_saddle.py",
    "data/4DNFIOZ1TRUS.mcool::/resolutions/100000",
    "saddle/e1-8a6b503ff4af.tsv",
    "50",
    "<out>",
    "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX"
   ],
   "out": "cooltools.npz",
   "env": null,
   "command": "python ../../scripts/cooltools_saddle.py data/4DNFIOZ1TRUS.mcool::/resolutions/100000 saddle/e1-8a6b503ff4af.tsv 50 saddle/cooltools.npz chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX"
  },
  {
   "name": "frip-peaks",
   "section": 22,
   "analysis": "Fraction of signal in features",
   "data": "mouse ATAC-seq, 2 replicates, chr19; § 5’s peaks and § 15’s promoters",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "ATAC-seq peaks",
   "group": "ATAC-seq peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "frip",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw",
    "--features",
    "yapc/seed0/yapc_0.05.bed",
    "--perFeature"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix frip --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features yapc/seed0/yapc_0.05.bed --perFeature --out frip/peaks"
  },
  {
   "name": "frip-promoters",
   "section": 22,
   "analysis": "Fraction of signal in features",
   "data": "mouse ATAC-seq, 2 replicates, chr19; § 5’s peaks and § 15’s promoters",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "promoters",
   "group": "promoters",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "frip",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw",
    "--features",
    "overlap/promoters.bed",
    "--perFeature"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix frip --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features overlap/promoters.bed --perFeature --out frip/promoters"
  },
  {
   "name": "pybigwig-frip-peaks",
   "section": 22,
   "analysis": "Fraction of signal in features",
   "data": "mouse ATAC-seq, 2 replicates, chr19; § 5’s peaks and § 15’s promoters",
   "tool": "pyBigWig, NumPy",
   "version": "0.3.26, 2.5.4",
   "variant": "ATAC-seq peaks",
   "group": "ATAC-seq peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_frip.py",
    "yapc/seed0/yapc_0.05.bed",
    "<out>",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw"
   ],
   "out": "pybigwig-peaks",
   "env": null,
   "command": "python ../../scripts/pybigwig_frip.py yapc/seed0/yapc_0.05.bed frip/pybigwig-peaks data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw"
  },
  {
   "name": "pybigwig-frip-promoters",
   "section": 22,
   "analysis": "Fraction of signal in features",
   "data": "mouse ATAC-seq, 2 replicates, chr19; § 5’s peaks and § 15’s promoters",
   "tool": "pyBigWig, NumPy",
   "version": "0.3.26, 2.5.4",
   "variant": "promoters",
   "group": "promoters",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_frip.py",
    "overlap/promoters.bed",
    "<out>",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw"
   ],
   "out": "pybigwig-promoters",
   "env": null,
   "command": "python ../../scripts/pybigwig_frip.py overlap/promoters.bed frip/pybigwig-promoters data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw"
  },
  {
   "name": "groupsignal-entries",
   "section": 23,
   "analysis": "Signal by group",
   "data": "mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "one value per entry",
   "group": "one value per entry",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "groupsignal",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw",
    "--features",
    "groupsignal/ab-fa907cf22489.bed",
    "--split",
    "name"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --out groupsignal/app-entries"
  },
  {
   "name": "groupsignal",
   "section": 23,
   "analysis": "Signal by group",
   "data": "mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "10 kb stretches",
   "group": "10 kb stretches",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "groupsignal",
    "--tracks",
    "data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw",
    "--features",
    "groupsignal/ab-fa907cf22489.bed",
    "--split",
    "name",
    "--resolution",
    "10000"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix groupsignal --tracks data/4DNFIIY4QW2D.chr19.bw,data/4DNFITBRHVZE.chr19.bw --features groupsignal/ab-fa907cf22489.bed --split name --resolution 10000 --out groupsignal/app"
  },
  {
   "name": "pybigwig-groupsignal-entries",
   "section": 23,
   "analysis": "Signal by group",
   "data": "mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "one value per entry",
   "group": "one value per entry",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_groupsignal.py",
    "groupsignal/ab-fa907cf22489.bed",
    "0",
    "<out>",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw"
   ],
   "out": "reference-entries",
   "env": null,
   "command": "python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 0 groupsignal/reference-entries data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw"
  },
  {
   "name": "pybigwig-groupsignal",
   "section": 23,
   "analysis": "Signal by group",
   "data": "mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches",
   "tool": "pyBigWig, SciPy",
   "version": "0.3.26, 1.16.3",
   "variant": "10 kb stretches",
   "group": "10 kb stretches",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/pybigwig_groupsignal.py",
    "groupsignal/ab-fa907cf22489.bed",
    "10000",
    "<out>",
    "data/4DNFIIY4QW2D.chr19.bw",
    "data/4DNFITBRHVZE.chr19.bw"
   ],
   "out": "reference",
   "env": null,
   "command": "python ../../scripts/pybigwig_groupsignal.py groupsignal/ab-fa907cf22489.bed 10000 groupsignal/reference data/4DNFIIY4QW2D.chr19.bw data/4DNFITBRHVZE.chr19.bw"
  },
  {
   "name": "gm-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "insulation, four scales",
   "group": "insulation",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "insulation",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "--window",
    "5",
    "--scales",
    "4"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix insulation data/4DNFIXP4QG5B_10000.chr19.cool --window 5 --scales 4 --out gm12878/insulation/app"
  },
  {
   "name": "gm-peaks",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "peaks",
   "group": "peaks",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "peaks",
    "--signal",
    "data/ENCFF734CUT.chr19.bw",
    "--replicate",
    "data/ENCFF644EEX.chr19.bw",
    "--perPeak",
    "--width",
    "150",
    "--times",
    "3",
    "--minWidth",
    "75",
    "--truncate",
    "100000",
    "--idr",
    "0.05"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix peaks --signal data/ENCFF734CUT.chr19.bw --replicate data/ENCFF644EEX.chr19.bw --perPeak --width 150 --times 3 --minWidth 75 --truncate 100000 --idr 0.05 --out gm12878/yapc/app"
  },
  {
   "name": "gm-apa-raw",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "APA, raw",
   "group": "APA",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "--anchors",
    "consecutive",
    "--features",
    "gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed",
    "--norm",
    "none",
    "--minDist",
    "12",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw"
  },
  {
   "name": "gm-apa-oe",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "APA, over the expected",
   "group": "APA",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "--anchors",
    "consecutive",
    "--features",
    "gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed",
    "--norm",
    "oe",
    "--minDist",
    "12",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm oe --minDist 12 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/oe"
  },
  {
   "name": "gm-apa-raw-every",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "APA, raw, every pair",
   "group": "APA",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "--anchors",
    "consecutive",
    "--features",
    "gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed",
    "--norm",
    "none",
    "--minDist",
    "0",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm none --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/raw-every"
  },
  {
   "name": "gm-apa-oe-every",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "APA, over the expected, every pair",
   "group": "APA",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "--anchors",
    "consecutive",
    "--features",
    "gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed",
    "--norm",
    "oe",
    "--minDist",
    "0",
    "--mode",
    "fixed",
    "--window",
    "5",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_10000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm oe --minDist 0 --mode fixed --window 5 --minDiag 2 --out gm12878/apa/oe-every"
  },
  {
   "name": "gm-apa-oe-2kb",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "APA at 2 kb, over the expected",
   "group": "APA",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_2000.chr19.cool",
    "--anchors",
    "consecutive",
    "--features",
    "gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed",
    "--norm",
    "oe",
    "--minDist",
    "22",
    "--mode",
    "fixed",
    "--window",
    "10",
    "--minDiag",
    "2"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_2000.chr19.cool --anchors consecutive --features gm12878/yapc/app/ENCFF734CUT.peaks.peaks-data_ENCFF734CUT_chr19_bw-data_ENCFF644EEX_chr19_bw.bed --norm oe --minDist 22 --mode fixed --window 10 --minDiag 2 --out gm12878/apa/oe-2kb"
  },
  {
   "name": "gm-apa-tads-oe",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "TADs, scaled, over the expected",
   "group": "APA",
   "threads": 1,
   "bench": false,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "apa",
    "data/4DNFIXP4QG5B_2000.chr19.cool",
    "--anchors",
    "features",
    "--features",
    "gm12878/apa/domains.bed",
    "--mode",
    "scaled",
    "--grid",
    "51",
    "--flankFraction",
    "0.5",
    "--minDiag",
    "2",
    "--norm",
    "oe"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix apa data/4DNFIXP4QG5B_2000.chr19.cool --anchors features --features gm12878/apa/domains.bed --mode scaled --grid 51 --flankFraction 0.5 --minDiag 2 --norm oe --out gm12878/apa/tads-oe"
  },
  {
   "name": "gm-metaplot-signal",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "metaplot, CTCF and ATAC-seq, ±2 kb",
   "group": "metaplot, signal",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "metaplot",
    "--tracks",
    "data/ENCFF734CUT.chr19.bw",
    "--tracks",
    "data/ENCFF644EEX.chr19.bw",
    "--tracks",
    "data/ENCFF487LOB.chr19.bw",
    "--features",
    "gm12878/metaplot/sites.bed",
    "--mode",
    "reference",
    "--at",
    "centre",
    "--stranded=false",
    "--flank",
    "2000",
    "--step",
    "50",
    "--band",
    "none"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix metaplot --tracks data/ENCFF734CUT.chr19.bw --tracks data/ENCFF644EEX.chr19.bw --tracks data/ENCFF487LOB.chr19.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 2000 --step 50 --band none --out gm12878/metaplot/app-signal"
  },
  {
   "name": "gm-metaplot-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "metaplot, insulation at four scales, ±500 kb",
   "group": "metaplot, insulation",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "metaplot",
    "--tracks",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw",
    "--tracks",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw",
    "--tracks",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw",
    "--tracks",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw",
    "--features",
    "gm12878/metaplot/sites.bed",
    "--mode",
    "reference",
    "--at",
    "centre",
    "--stranded=false",
    "--flank",
    "500000",
    "--step",
    "10000",
    "--band",
    "none"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix metaplot --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw --tracks gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw --features gm12878/metaplot/sites.bed --mode reference --at centre --stranded=false --flank 500000 --step 10000 --band none --out gm12878/metaplot/app-insulation"
  },
  {
   "name": "gm-cooltools-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "insulation, four scales",
   "group": "insulation",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_insulation_scales.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "<out>",
    "4",
    "50000",
    "100000",
    "200000",
    "400000"
   ],
   "out": "cooltools.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_insulation_scales.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/insulation/cooltools.tsv 4 50000 100000 200000 400000"
  },
  {
   "name": "gm-yapc-seed0",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "peaks, seed 0",
   "group": "peaks",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "0",
    "<out>",
    "cond",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 0 gm12878/yapc/seed0/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "gm-yapc-seed1",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "peaks, seed 1",
   "group": "peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "1",
    "<out>",
    "cond",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 1 gm12878/yapc/seed1/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "gm-yapc-seed2",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "peaks, seed 2",
   "group": "peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "2",
    "<out>",
    "cond",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 2 gm12878/yapc/seed2/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "gm-yapc-seed3",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "peaks, seed 3",
   "group": "peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "3",
    "<out>",
    "cond",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 3 gm12878/yapc/seed3/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "gm-yapc-seed4",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "yapc 0.1",
   "version": "0.1, with idr 2.0.3",
   "variant": "peaks, seed 4",
   "group": "peaks",
   "threads": 1,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/yapc-env/bin/python",
    "../../scripts/yapc_idr.py",
    "4",
    "<out>",
    "cond",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "--smoothing-window-width",
    "150",
    "--smoothing-times",
    "3",
    "--min-concave-region-width",
    "75",
    "--truncate-idr-input",
    "100000"
   ],
   "out": "yapc",
   "env": {
    "PATH": "/home/runner/work/_temp/yapc-env/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "yapc-env/bin/python ../../scripts/yapc_idr.py 4 gm12878/yapc/seed4/yapc cond data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw --smoothing-window-width 150 --smoothing-times 3 --min-concave-region-width 75 --truncate-idr-input 100000"
  },
  {
   "name": "gm-expected",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "the expected, for coolpuppy",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_expected_cis.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "<out>",
    "4"
   ],
   "out": "expected.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_expected_cis.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/expected.tsv 4"
  },
  {
   "name": "gm-coolpuppy-raw",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "APA, raw",
   "group": "APA",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "gm12878/apa/consecutive.bedpe",
    "50000",
    "<out>",
    "4"
   ],
   "out": "coolpuppy-raw.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw.tsv 4"
  },
  {
   "name": "gm-coolpuppy-oe",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "APA, over the expected",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "gm12878/apa/consecutive.bedpe",
    "50000",
    "<out>",
    "4",
    "--expected",
    "gm12878/apa/expected.tsv"
   ],
   "out": "coolpuppy-oe.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-oe.tsv 4 --expected gm12878/apa/expected.tsv"
  },
  {
   "name": "gm-coolpuppy-raw-every",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "APA, raw, every pair",
   "group": "APA",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "gm12878/apa/consecutive.bedpe",
    "50000",
    "<out>",
    "4",
    "--mindist",
    "0"
   ],
   "out": "coolpuppy-raw-every.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-raw-every.tsv 4 --mindist 0"
  },
  {
   "name": "gm-coolpuppy-oe-every",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "APA, over the expected, every pair",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_10000.chr19.cool",
    "gm12878/apa/consecutive.bedpe",
    "50000",
    "<out>",
    "4",
    "--expected",
    "gm12878/apa/expected.tsv",
    "--mindist",
    "0"
   ],
   "out": "coolpuppy-oe-every.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_10000.chr19.cool gm12878/apa/consecutive.bedpe 50000 gm12878/apa/coolpuppy-oe-every.tsv 4 --expected gm12878/apa/expected.tsv --mindist 0"
  },
  {
   "name": "gm-expected-2kb",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "the expected at 2 kb, for coolpuppy",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_expected_cis.py",
    "data/4DNFIXP4QG5B_2000.chr19.cool",
    "<out>",
    "4"
   ],
   "out": "expected-2kb.tsv",
   "env": null,
   "command": "python ../../scripts/cooltools_expected_cis.py data/4DNFIXP4QG5B_2000.chr19.cool gm12878/apa/expected-2kb.tsv 4"
  },
  {
   "name": "gm-coolpuppy-oe-2kb",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "APA at 2 kb, over the expected",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_2000.chr19.cool",
    "gm12878/apa/consecutive.bedpe",
    "20000",
    "<out>",
    "4",
    "--expected",
    "gm12878/apa/expected-2kb.tsv"
   ],
   "out": "coolpuppy-oe-2kb.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_2000.chr19.cool gm12878/apa/consecutive.bedpe 20000 gm12878/apa/coolpuppy-oe-2kb.tsv 4 --expected gm12878/apa/expected-2kb.tsv"
  },
  {
   "name": "gm-coolpuppy-tads-oe",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "coolpuppy",
   "version": "1.1.0",
   "variant": "TADs, scaled, over the expected",
   "group": "APA",
   "threads": 4,
   "bench": false,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/coolpuppy_pileup.py",
    "data/4DNFIXP4QG5B_2000.chr19.cool",
    "gm12878/apa/domains.bed",
    "100000",
    "<out>",
    "4",
    "--local",
    "--expected",
    "gm12878/apa/expected-2kb.tsv",
    "--rescale-flank",
    "0.5",
    "--rescale-size",
    "51"
   ],
   "out": "coolpuppy-tads-oe.tsv",
   "env": null,
   "command": "python ../../scripts/coolpuppy_pileup.py data/4DNFIXP4QG5B_2000.chr19.cool gm12878/apa/domains.bed 100000 gm12878/apa/coolpuppy-tads-oe.tsv 4 --local --expected gm12878/apa/expected-2kb.tsv --rescale-flank 0.5 --rescale-size 51"
  },
  {
   "name": "gm-computematrix-signal",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "computeMatrix",
   "group": "metaplot, signal",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/computeMatrix",
    "reference-point",
    "-S",
    "data/ENCFF734CUT.chr19.bw",
    "data/ENCFF644EEX.chr19.bw",
    "data/ENCFF487LOB.chr19.bw",
    "-R",
    "gm12878/metaplot/sites.bed",
    "--referencePoint",
    "center",
    "-b",
    "2000",
    "-a",
    "2000",
    "--binSize",
    "50",
    "-p",
    "4",
    "-o",
    "<out>"
   ],
   "out": "deeptools-signal.mat.gz",
   "env": null,
   "command": "computeMatrix reference-point -S data/ENCFF734CUT.chr19.bw data/ENCFF644EEX.chr19.bw data/ENCFF487LOB.chr19.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 2000 -a 2000 --binSize 50 -p 4 -o gm12878/metaplot/deeptools-signal.mat.gz"
  },
  {
   "name": "gm-plotprofile-signal",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotProfile",
   "group": "metaplot, signal",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotProfile",
    "-m",
    "gm12878/metaplot/deeptools-signal.mat.gz",
    "-out",
    "<out>.png",
    "--outFileNameData",
    "<out>.tab"
   ],
   "out": "deeptools-signal-profile",
   "env": null,
   "command": "plotProfile -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-profile.png --outFileNameData gm12878/metaplot/deeptools-signal-profile.tab"
  },
  {
   "name": "gm-plotheatmap-signal",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotHeatmap",
   "group": "metaplot, signal",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotHeatmap",
    "-m",
    "gm12878/metaplot/deeptools-signal.mat.gz",
    "-out",
    "<out>.png",
    "--outFileSortedRegions",
    "<out>.bed"
   ],
   "out": "deeptools-signal-heatmap",
   "env": null,
   "command": "plotHeatmap -m gm12878/metaplot/deeptools-signal.mat.gz -out gm12878/metaplot/deeptools-signal-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-signal-heatmap.bed"
  },
  {
   "name": "gm-computematrix-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "computeMatrix",
   "group": "metaplot, insulation",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/computeMatrix",
    "reference-point",
    "-S",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw",
    "gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw",
    "-R",
    "gm12878/metaplot/sites.bed",
    "--referencePoint",
    "center",
    "-b",
    "500000",
    "-a",
    "500000",
    "--binSize",
    "10000",
    "-p",
    "4",
    "-o",
    "<out>"
   ],
   "out": "deeptools-insulation.mat.gz",
   "env": null,
   "command": "computeMatrix reference-point -S gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w5.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w10.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w20.bw gm12878/insulation/app/4DNFIXP4QG5B_10000.insulation.insulation-w40.bw -R gm12878/metaplot/sites.bed --referencePoint center -b 500000 -a 500000 --binSize 10000 -p 4 -o gm12878/metaplot/deeptools-insulation.mat.gz"
  },
  {
   "name": "gm-plotprofile-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotProfile",
   "group": "metaplot, insulation",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotProfile",
    "-m",
    "gm12878/metaplot/deeptools-insulation.mat.gz",
    "-out",
    "<out>.png",
    "--outFileNameData",
    "<out>.tab"
   ],
   "out": "deeptools-insulation-profile",
   "env": null,
   "command": "plotProfile -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-profile.png --outFileNameData gm12878/metaplot/deeptools-insulation-profile.tab"
  },
  {
   "name": "gm-plotheatmap-insulation",
   "section": 24,
   "analysis": "CTCF sites in GM12878 (Fig. 2)",
   "data": "GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19",
   "tool": "deepTools",
   "version": "4.0.0",
   "variant": "plotHeatmap",
   "group": "metaplot, insulation",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/plotHeatmap",
    "-m",
    "gm12878/metaplot/deeptools-insulation.mat.gz",
    "-out",
    "<out>.png",
    "--outFileSortedRegions",
    "<out>.bed"
   ],
   "out": "deeptools-insulation-heatmap",
   "env": null,
   "command": "plotHeatmap -m gm12878/metaplot/deeptools-insulation.mat.gz -out gm12878/metaplot/deeptools-insulation-heatmap.png --outFileSortedRegions gm12878/metaplot/deeptools-insulation-heatmap.bed"
  },
  {
   "name": "pairstats",
   "section": 25,
   "analysis": "Pairs statistics",
   "data": "yeast Hi-C contact list, deduplicated",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "stats",
    "data/CH128.pairs.gz"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix stats data/CH128.pairs.gz --out pairstats/app"
  },
  {
   "name": "pairtools-stats",
   "section": 25,
   "analysis": "Pairs statistics",
   "data": "yeast Hi-C contact list, deduplicated",
   "tool": "pairtools",
   "version": "1.1.2",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/pairtools-env/bin/pairtools",
    "stats",
    "data/CH128.pairs.gz",
    "-o",
    "<out>"
   ],
   "out": "pairtools.stats",
   "env": {
    "MPLBACKEND": "agg"
   },
   "command": "pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats"
  },
  {
   "name": "restriction",
   "section": 26,
   "analysis": "Restriction sites",
   "data": "yeast R64-1-1, DpnII, 5 kb bins",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "restriction",
    "restriction/CH128.5000.cool",
    "--sequence",
    "data/R64-1-1.fa",
    "--enzyme",
    "DpnII"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix restriction restriction/CH128.5000.cool --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-sites"
  },
  {
   "name": "bioframe-digest",
   "section": 26,
   "analysis": "Restriction sites",
   "data": "yeast R64-1-1, DpnII, 5 kb bins",
   "tool": "bioframe, Biopython",
   "version": "0.8.0, 1.88",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/bioframe_digest.py",
    "data/R64-1-1.fa",
    "DpnII",
    "5000",
    "<out>",
    "-2"
   ],
   "out": "digest",
   "env": null,
   "command": "python ../../scripts/bioframe_digest.py data/R64-1-1.fa DpnII 5000 restriction/digest -2"
  },
  {
   "name": "pairsqc",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "pairsqc",
    "data/CH128.pairs.gz",
    "--bin-size",
    "5000",
    "--sequence",
    "data/R64-1-1.fa",
    "--enzyme",
    "DpnII"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix pairsqc data/CH128.pairs.gz --bin-size 5000 --sequence data/R64-1-1.fa --enzyme DpnII --out restriction/app-pairsqc"
  },
  {
   "name": "cooler-cload",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "cooler",
   "version": "0.10.4",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "cooler",
    "cload",
    "pairs",
    "-c1",
    "2",
    "-p1",
    "3",
    "-c2",
    "4",
    "-p2",
    "5",
    "data/R64-1-1.chrom.sizes:5000",
    "data/CH128.pairs.gz",
    "<out>"
   ],
   "out": "CH128.5000.cool",
   "env": {
    "PATH": "/home/runner/work/_temp/refs/bin:/home/runner/work/_temp/refs/bin:/opt/hostedtoolcache/Python/3.13.17/x64/bin:/opt/hostedtoolcache/Python/3.13.17/x64:/opt/hostedtoolcache/Python/3.12.15/x64/bin:/opt/hostedtoolcache/Python/3.12.15/x64:/opt/hostedtoolcache/Python/3.11.17/x64/bin:/opt/hostedtoolcache/Python/3.11.17/x64:/opt/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.13-9.0.LTS/x64/bin:/opt/hostedtoolcache/node/24.22.1/x64/bin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"
   },
   "command": "cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 data/R64-1-1.chrom.sizes:5000 data/CH128.pairs.gz restriction/CH128.5000.cool"
  },
  {
   "name": "pairtools-restrict-top",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "pairtools",
   "version": "1.1.2",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/pairtools-env/bin/pairtools",
    "restrict",
    "-f",
    "restriction/digest.frags.bed",
    "data/CH128.pairs.gz",
    "-o",
    "<out>"
   ],
   "out": "CH128.restricted.pairs.gz",
   "env": {
    "MPLBACKEND": "agg"
   },
   "command": "pairtools restrict -f restriction/digest.frags.bed data/CH128.pairs.gz -o restriction/CH128.restricted.pairs.gz"
  },
  {
   "name": "pairtools-restrict-bottom",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "pairtools",
   "version": "1.1.2",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/pairtools-env/bin/pairtools",
    "restrict",
    "-f",
    "restriction/digest.frags-bottom.bed",
    "data/CH128.pairs.gz",
    "-o",
    "<out>"
   ],
   "out": "CH128.restricted-bottom.pairs.gz",
   "env": {
    "MPLBACKEND": "agg"
   },
   "command": "pairtools restrict -f restriction/digest.frags-bottom.bed data/CH128.pairs.gz -o restriction/CH128.restricted-bottom.pairs.gz"
  },
  {
   "name": "restriction-reference",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "pandas",
   "version": "2.3.3",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/restriction_reference.py",
    "data/R64-1-1.fa",
    "DpnII",
    "restriction/CH128.restricted.pairs.gz",
    "restriction/CH128.restricted-bottom.pairs.gz",
    "<out>",
    "-2"
   ],
   "out": "pairtools",
   "env": null,
   "command": "python ../../scripts/restriction_reference.py data/R64-1-1.fa DpnII restriction/CH128.restricted.pairs.gz restriction/CH128.restricted-bottom.pairs.gz restriction/pairtools -2"
  },
  {
   "name": "cooltools-coverage-sites",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "cooltools",
   "version": "0.7.1",
   "variant": "",
   "group": "",
   "threads": 4,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/cooltools_coverage_sites.py",
    "restriction/CH128.5000.cool",
    "restriction/digest.sites.tsv",
    "<out>",
    "4"
   ],
   "out": "coverage",
   "env": null,
   "command": "python ../../scripts/cooltools_coverage_sites.py restriction/CH128.5000.cool restriction/digest.sites.tsv restriction/coverage 4"
  },
  {
   "name": "pairsqc-pairtools-stats",
   "section": 27,
   "analysis": "Pairs QC",
   "data": "§ 25's contact list against § 26's DpnII sites, 5 kb",
   "tool": "pairtools",
   "version": "1.1.2",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/pairtools-env/bin/pairtools",
    "stats",
    "data/CH128.pairs.gz",
    "-o",
    "<out>"
   ],
   "out": "pairtools.stats",
   "env": {
    "MPLBACKEND": "agg"
   },
   "command": "pairtools stats data/CH128.pairs.gz -o pairstats/pairtools.stats"
  },
  {
   "name": "arrowhead-raw",
   "section": 28,
   "analysis": "TAD annotation",
   "data": "K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "raw",
   "group": "raw",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "arrowhead",
    "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000",
    "--sequences",
    "21,22",
    "--no-balance"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --no-balance --out arrowhead/app-raw"
  },
  {
   "name": "arrowhead-balanced",
   "section": 28,
   "analysis": "TAD annotation",
   "data": "K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "balanced",
   "group": "balanced",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "arrowhead",
    "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000",
    "--sequences",
    "21,22"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix arrowhead https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic::/resolutions/10000 --sequences 21,22 --out arrowhead/app-balanced"
  },
  {
   "name": "juicer-arrowhead-raw",
   "section": 28,
   "analysis": "TAD annotation",
   "data": "K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR",
   "tool": "Juicer Tools",
   "version": "1.22.01, on Java 21.0.13",
   "variant": "raw",
   "group": "raw",
   "threads": 1,
   "bench": true,
   "argv": [
    "java",
    "-Xmx8g",
    "-jar",
    "data/juicer_tools_1.22.01.jar",
    "arrowhead",
    "-c",
    "21,22",
    "-m",
    "2000",
    "-r",
    "10000",
    "-k",
    "NONE",
    "--threads",
    "1",
    "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic",
    "<out>"
   ],
   "out": "juicer-raw",
   "env": null,
   "command": "java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k NONE --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-raw"
  },
  {
   "name": "juicer-arrowhead-balanced",
   "section": 28,
   "analysis": "TAD annotation",
   "data": "K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR",
   "tool": "Juicer Tools",
   "version": "1.22.01, on Java 21.0.13",
   "variant": "balanced",
   "group": "balanced",
   "threads": 1,
   "bench": true,
   "argv": [
    "java",
    "-Xmx8g",
    "-jar",
    "data/juicer_tools_1.22.01.jar",
    "arrowhead",
    "-c",
    "21,22",
    "-m",
    "2000",
    "-r",
    "10000",
    "-k",
    "KR",
    "--threads",
    "1",
    "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic",
    "<out>"
   ],
   "out": "juicer-balanced",
   "env": null,
   "command": "java -Xmx8g -jar data/juicer_tools_1.22.01.jar arrowhead -c 21,22 -m 2000 -r 10000 -k KR --threads 1 https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcfcb009-f006-4ab8-a4c7-af72be58c12c/4DNFITUOMFUQ.hic arrowhead/juicer-balanced"
  },
  {
   "name": "mapreport",
   "section": 29,
   "analysis": "Map report",
   "data": "yeast Micro-C, every stored resolution",
   "tool": "chromosomix",
   "version": "0.19.0 at 997e59c",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "node",
    "/home/runner/work/chromosomix/chromosomix/dist-cli/chromosomix.mjs",
    "mapreport",
    "data/GSE151553_A364_merged.mcool::/resolutions/800"
   ],
   "out": null,
   "env": null,
   "command": "chromosomix mapreport data/GSE151553_A364_merged.mcool::/resolutions/800 --out mapreport/app"
  },
  {
   "name": "map-resolution",
   "section": 29,
   "analysis": "Map report",
   "data": "yeast Micro-C, every stored resolution",
   "tool": "cooler",
   "version": "0.10.4",
   "variant": "",
   "group": "",
   "threads": 1,
   "bench": true,
   "argv": [
    "/home/runner/work/_temp/refs/bin/python",
    "../../scripts/map_resolution.py",
    "data/GSE151553_A364_merged.mcool",
    "<out>"
   ],
   "out": "cooler.tsv",
   "env": null,
   "command": "python ../../scripts/map_resolution.py data/GSE151553_A364_merged.mcool mapreport/cooler.tsv"
  }
 ]
}