{"@id":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"81555a89cc2d16bd3ab131a6685a44b44f08f927","path":"v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl"},"retrievedOn":"2026-09-22T15:31:35.567+00:00","lastCommit":"81555a89cc2d16bd3ab131a6685a44b44f08f927","label":"04-peakcall-pe.cwl","doc":"ATAC-seq 04 quantification - PE","inputs":{"nthreads":{"type":"Integer"},"input_bam_files":{"type":"File[]"},"as_narrowPeak_file":{"doc":"Definition narrowPeak file in AutoSql format (used in bedToBigBed)","type":"File"},"input_genome_sizes":{"doc":"Two column tab-delimited file with chromosome size information","type":"File"},"genome_effective_size":{"doc":"Effective genome size used by MACS2. It can be numeric or a shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs","type":"String"}},"outputs":{"output_peak_file":{"doc":"peakshift/phantomPeak results file","type":"File[]"},"output_peak_xls_file":{"doc":"Peak calling report file (*_peaks.xls file produced by MACS2)","type":"File[]"},"output_peak_bigbed_file":{"doc":"Peaks in bigBed format","type":"File[]"},"output_spp_x_cross_corr":{"doc":"peakshift/phantomPeak results file","type":"File[]"},"output_peak_summits_file":{"doc":"File containing peak summits","type":"File[]"},"output_extended_peak_file":{"doc":"peakshift/phantomPeak extended fragment results file","type":"File[]"},"output_unpaired_peak_file":{"doc":"peakshift/phantomPeak results file using each paired mate independently","type":"File[]"},"output_spp_cross_corr_plot":{"doc":"peakshift/phantomPeak results file","type":"File[]"},"output_unpaired_peak_xls_file":{"doc":"Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently","type":"File[]"},"output_filtered_read_count_file":{"doc":"Filtered read count reported by MACS2","type":"File[]"},"output_unpaired_peak_bigbed_file":{"doc":"Peaks in bigBed format using each paired mate independently","type":"File[]"},"output_unpaired_peak_summits_file":{"doc":"File containing peak summits using each paired mate independently","type":"File[]"},"output_peak_count_within_replicate":{"doc":"Peak counts within replicate","type":"File[]"},"output_unpaired_extended_peak_file":{"doc":"peakshift/phantomPeak extended fragment results file using each paired mate independently","type":"File[]"},"output_unpaired_filtered_read_count_file":{"doc":"Filtered read count reported by MACS2 using each paired mate independently","type":"File[]"},"output_read_in_peak_count_within_replicate":{"doc":"Reads peak counts within replicate","type":"File[]"},"output_unpaired_peak_count_within_replicate":{"doc":"Peak counts within replicate using each paired mate independently","type":"File[]"}},"steps":{"spp":{"run":"../spp/spp.cwl","runType":"COMMANDLINETOOL","sources":{"spp":{"sourceIDs":["input_bam_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#spp/nthreads":{"sourceIDs":["nthreads"]}}},"count-peaks":{"doc":"Counts lines in a file and returns a suffixed file with that number","run":"../utils/count-with-output-suffix.cwl","runType":"COMMANDLINETOOL","sources":{"count-peaks":{"sourceIDs":["peak-calling"]}}},"peak-calling":{"run":"../peak_calling/macs2-callpeak.cwl","runType":"COMMANDLINETOOL","sources":{"peak-calling":{"sourceIDs":["genome_effective_size"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peak-calling/treatment":{"sourceIDs":["input_bam_files"]}}},"unpair_bedpe":{"doc":"Un-pack a BEDPE concatenating both mates so that they are treated independently","run":"../peak_calling/bedpe-to-bed.cwl","runType":"COMMANDLINETOOL","sources":{"unpair_bedpe":{"sourceIDs":["bedtools_bamtobed"]}}},"clip-off-chrom":{"doc":"\\\"Tool:   bedClip - Remove lines from bed file that refer to off-chromosome places.\nusage:\n   bedClip input.bed chrom.sizes output.bed\nchrom.sizes is a two-column file/URL: <chromosome name> <size in bases>\nIf the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like\n  http://hgdownload.cse.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes\nor you may use the script fetchChromSizes to download the chrom.sizes file.\nIf not hosted by UCSC, a chrom.sizes file can be generated by running\ntwoBitInfo on the assembly .2bit file.\noptions:\n   -verbose=2 - set to get list of lines clipped and why\\\"\n","run":"../quant/bedClip.cwl","runType":"COMMANDLINETOOL","sources":{"clip-off-chrom":{"sourceIDs":["input_genome_sizes"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#clip-off-chrom/bed_file":{"sourceIDs":["trunk-peak-score-unpaired"]}}},"sort-bam-by-name":{"run":"../map/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort-bam-by-name":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#sort-bam-by-name/input_file":{"sourceIDs":["input_bam_files"]}}},"trunk-peak-score":{"doc":"Trunk scores in ENCODE bed6+4 files","run":"../utils/trunk-peak-score.cwl","runType":"COMMANDLINETOOL","sources":{"trunk-peak-score":{"sourceIDs":["peak-calling"]}}},"bedtools_bamtobed":{"run":"../map/bedtools-bamtobed.cwl","runType":"COMMANDLINETOOL","sources":{"bedtools_bamtobed":{"sourceIDs":["sort-bam-by-name"]}}},"peaks-bed-to-bigbed":{"doc":"\\\"bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4)\nusage:\n   bedToBigBed in.bed chrom.sizes out.bb\nWhere in.bed is in one of the ascii bed formats, but not including track lines\nand chrom.sizes is two column: <chromosome name> <size in bases>\nand out.bb is the output indexed big bed file.\nUse the script: fetchChromSizes to obtain the actual chrom.sizes information\nfrom UCSC, please do not make up a chrom sizes from your own information.\nThe in.bed file must be sorted by chromosome,start,\n  to sort a bed file, use the unix sort command:\n     sort -k1,1 -k2,2n unsorted.bed > sorted.bed\\\"\n","run":"../quant/bedToBigBed.cwl","runType":"COMMANDLINETOOL","sources":{"peaks-bed-to-bigbed":{"sourceIDs":["as_narrowPeak_file"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peaks-bed-to-bigbed/bed":{"sourceIDs":["trunk-peak-score"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peaks-bed-to-bigbed/genome_sizes":{"sourceIDs":["input_genome_sizes"]}}},"count-peaks-unpaired":{"doc":"Counts lines in a file and returns a suffixed file with that number","run":"../utils/count-with-output-suffix.cwl","runType":"COMMANDLINETOOL","sources":{"count-peaks-unpaired":{"sourceIDs":["peak-calling-unpaired"]}}},"count-reads-filtered":{"doc":"Count number of dedup-ed reads used in peak calling","run":"../peak_calling/count-reads-after-filtering.cwl","runType":"COMMANDLINETOOL","sources":{"count-reads-filtered":{"sourceIDs":["peak-calling"]}}},"filter-reads-in-peaks":{"doc":"Filter BAM file to only include reads overlapping with a BED file","run":"../peak_calling/samtools-filter-in-bedfile.cwl","runType":"COMMANDLINETOOL","sources":{"filter-reads-in-peaks":{"sourceIDs":["input_bam_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#filter-reads-in-peaks/input_bedfile":{"sourceIDs":["peak-calling"]}}},"peak-calling-unpaired":{"run":"../peak_calling/macs2-callpeak.cwl","runType":"COMMANDLINETOOL","sources":{"peak-calling-unpaired":{"sourceIDs":["unpair_bedpe"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peak-calling-unpaired/g":{"sourceIDs":["genome_effective_size"]}}},"extract-peak-frag-length":{"doc":"Extracts best fragment length from SPP output text file","run":"../spp/extract-best-frag-length.cwl","runType":"COMMANDLINETOOL","sources":{"extract-peak-frag-length":{"sourceIDs":["spp"]}}},"trunk-peak-score-unpaired":{"doc":"Trunk scores in ENCODE bed6+4 files","run":"../utils/trunk-peak-score.cwl","runType":"COMMANDLINETOOL","sources":{"trunk-peak-score-unpaired":{"sourceIDs":["peak-calling-unpaired"]}}},"extract-count-reads-in-peaks":{"doc":"Extract mapped reads from BAM file using Samtools flagstat command","run":"../peak_calling/samtools-extract-number-mapped-reads.cwl","runType":"COMMANDLINETOOL","sources":{"extract-count-reads-in-peaks":{"sourceIDs":["filter-reads-in-peaks"]}}},"peaks-bed-to-bigbed-unpaired":{"doc":"\\\"bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4)\nusage:\n   bedToBigBed in.bed chrom.sizes out.bb\nWhere in.bed is in one of the ascii bed formats, but not including track lines\nand chrom.sizes is two column: <chromosome name> <size in bases>\nand out.bb is the output indexed big bed file.\nUse the script: fetchChromSizes to obtain the actual chrom.sizes information\nfrom UCSC, please do not make up a chrom sizes from your own information.\nThe in.bed file must be sorted by chromosome,start,\n  to sort a bed file, use the unix sort command:\n     sort -k1,1 -k2,2n unsorted.bed > sorted.bed\\\"\n","run":"../quant/bedToBigBed.cwl","runType":"COMMANDLINETOOL","sources":{"peaks-bed-to-bigbed-unpaired":{"sourceIDs":["input_genome_sizes"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peaks-bed-to-bigbed-unpaired/as":{"sourceIDs":["as_narrowPeak_file"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#peaks-bed-to-bigbed-unpaired/bed":{"sourceIDs":["clip-off-chrom"]}}},"count-reads-filtered-unpaired":{"doc":"Count number of dedup-ed reads used in peak calling","run":"../peak_calling/count-reads-after-filtering.cwl","runType":"COMMANDLINETOOL","sources":{"count-reads-filtered-unpaired":{"sourceIDs":["peak-calling-unpaired"]}}},"filter-reads-in-peaks-unpaired":{"doc":"Filter BAM file to only include reads overlapping with a BED file","run":"../peak_calling/samtools-filter-in-bedfile.cwl","runType":"COMMANDLINETOOL","sources":{"filter-reads-in-peaks-unpaired":{"sourceIDs":["peak-calling-unpaired"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl#filter-reads-in-peaks-unpaired/input_bam_file":{"sourceIDs":["input_bam_files"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"as_narrowPeak_file\" [fillcolor=\"#94DDF4\",label=\"as_narrowPeak_file\"];\n    \"input_genome_sizes\" [fillcolor=\"#94DDF4\",label=\"input_genome_sizes\"];\n    \"input_bam_files\" [fillcolor=\"#94DDF4\",label=\"input_bam_files\"];\n    \"genome_effective_size\" [fillcolor=\"#94DDF4\",label=\"genome_effective_size\"];\n    \"nthreads\" [fillcolor=\"#94DDF4\",label=\"nthreads\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"output_unpaired_peak_bigbed_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_peak_bigbed_file\"];\n    \"output_peak_count_within_replicate\" [fillcolor=\"#94DDF4\",label=\"output_peak_count_within_replicate\"];\n    \"output_peak_summits_file\" [fillcolor=\"#94DDF4\",label=\"output_peak_summits_file\"];\n    \"output_unpaired_peak_summits_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_peak_summits_file\"];\n    \"output_unpaired_extended_peak_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_extended_peak_file\"];\n    \"output_peak_xls_file\" [fillcolor=\"#94DDF4\",label=\"output_peak_xls_file\"];\n    \"output_unpaired_peak_count_within_replicate\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_peak_count_within_replicate\"];\n    \"output_unpaired_peak_xls_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_peak_xls_file\"];\n    \"output_peak_bigbed_file\" [fillcolor=\"#94DDF4\",label=\"output_peak_bigbed_file\"];\n    \"output_spp_cross_corr_plot\" [fillcolor=\"#94DDF4\",label=\"output_spp_cross_corr_plot\"];\n    \"output_spp_x_cross_corr\" [fillcolor=\"#94DDF4\",label=\"output_spp_x_cross_corr\"];\n    \"output_unpaired_filtered_read_count_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_filtered_read_count_file\"];\n    \"output_read_in_peak_count_within_replicate\" [fillcolor=\"#94DDF4\",label=\"output_read_in_peak_count_within_replicate\"];\n    \"output_extended_peak_file\" [fillcolor=\"#94DDF4\",label=\"output_extended_peak_file\"];\n    \"output_peak_file\" [fillcolor=\"#94DDF4\",label=\"output_peak_file\"];\n    \"output_filtered_read_count_file\" [fillcolor=\"#94DDF4\",label=\"output_filtered_read_count_file\"];\n    \"output_unpaired_peak_file\" [fillcolor=\"#94DDF4\",label=\"output_unpaired_peak_file\"];\n  }\n  \"extract-count-reads-in-peaks\" [label=\"extract-count-reads-in-peaks\"];\n  \"clip-off-chrom\" [label=\"clip-off-chrom\"];\n  \"sort-bam-by-name\" [label=\"sort-bam-by-name\"];\n  \"peak-calling\" [label=\"peak-calling\"];\n  \"bedtools_bamtobed\" [label=\"bedtools_bamtobed\"];\n  \"peaks-bed-to-bigbed-unpaired\" [label=\"peaks-bed-to-bigbed-unpaired\"];\n  \"extract-peak-frag-length\" [label=\"extract-peak-frag-length\"];\n  \"peaks-bed-to-bigbed\" [label=\"peaks-bed-to-bigbed\"];\n  \"spp\" [label=\"spp\"];\n  \"count-reads-filtered\" [label=\"count-reads-filtered\"];\n  \"count-peaks\" [label=\"count-peaks\"];\n  \"filter-reads-in-peaks\" [label=\"filter-reads-in-peaks\"];\n  \"unpair_bedpe\" [label=\"unpair_bedpe\"];\n  \"filter-reads-in-peaks-unpaired\" [label=\"filter-reads-in-peaks-unpaired\"];\n  \"count-peaks-unpaired\" [label=\"count-peaks-unpaired\"];\n  \"trunk-peak-score\" [label=\"trunk-peak-score\"];\n  \"trunk-peak-score-unpaired\" [label=\"trunk-peak-score-unpaired\"];\n  \"count-reads-filtered-unpaired\" [label=\"count-reads-filtered-unpaired\"];\n  \"peak-calling-unpaired\" [label=\"peak-calling-unpaired\"];\n  \"filter-reads-in-peaks\" -> \"extract-count-reads-in-peaks\" [label=\"input_bam_file\"];\n  \"input_genome_sizes\" -> \"clip-off-chrom\" [label=\"genome_sizes\"];\n  \"trunk-peak-score-unpaired\" -> \"clip-off-chrom\" [label=\"bed_file\"];\n  \"nthreads\" -> \"sort-bam-by-name\" [label=\"nthreads\"];\n  \"input_bam_files\" -> \"sort-bam-by-name\" [label=\"input_file\"];\n  \"genome_effective_size\" -> \"peak-calling\" [label=\"g\"];\n  \"input_bam_files\" -> \"peak-calling\" [label=\"treatment\"];\n  \"sort-bam-by-name\" -> \"bedtools_bamtobed\" [label=\"bam\"];\n  \"input_genome_sizes\" -> \"peaks-bed-to-bigbed-unpaired\" [label=\"genome_sizes\"];\n  \"clip-off-chrom\" -> \"peaks-bed-to-bigbed-unpaired\" [label=\"bed\"];\n  \"as_narrowPeak_file\" -> \"peaks-bed-to-bigbed-unpaired\" [label=\"as\"];\n  \"spp\" -> \"extract-peak-frag-length\" [label=\"input_spp_txt_file\"];\n  \"as_narrowPeak_file\" -> \"peaks-bed-to-bigbed\" [label=\"as\"];\n  \"input_genome_sizes\" -> \"peaks-bed-to-bigbed\" [label=\"genome_sizes\"];\n  \"trunk-peak-score\" -> \"peaks-bed-to-bigbed\" [label=\"bed\"];\n  \"input_bam_files\" -> \"spp\" [label=\"input_bam\"];\n  \"nthreads\" -> \"spp\" [label=\"nthreads\"];\n  \"peak-calling\" -> \"count-reads-filtered\" [label=\"peak_xls_file\"];\n  \"peak-calling\" -> \"count-peaks\" [label=\"input_file\"];\n  \"input_bam_files\" -> \"filter-reads-in-peaks\" [label=\"input_bam_file\"];\n  \"peak-calling\" -> \"filter-reads-in-peaks\" [label=\"input_bedfile\"];\n  \"bedtools_bamtobed\" -> \"unpair_bedpe\" [label=\"bedpe\"];\n  \"peak-calling-unpaired\" -> \"filter-reads-in-peaks-unpaired\" [label=\"input_bedfile\"];\n  \"input_bam_files\" -> \"filter-reads-in-peaks-unpaired\" [label=\"input_bam_file\"];\n  \"peak-calling-unpaired\" -> \"count-peaks-unpaired\" [label=\"input_file\"];\n  \"peak-calling\" -> \"trunk-peak-score\" [label=\"peaks\"];\n  \"peak-calling-unpaired\" -> \"trunk-peak-score-unpaired\" [label=\"peaks\"];\n  \"peak-calling-unpaired\" -> \"count-reads-filtered-unpaired\" [label=\"peak_xls_file\"];\n  \"unpair_bedpe\" -> \"peak-calling-unpaired\" [label=\"treatment\"];\n  \"genome_effective_size\" -> \"peak-calling-unpaired\" [label=\"g\"];\n  \"peaks-bed-to-bigbed-unpaired\" -> \"output_unpaired_peak_bigbed_file\";\n  \"count-peaks\" -> \"output_peak_count_within_replicate\";\n  \"peak-calling\" -> \"output_peak_summits_file\";\n  \"peak-calling-unpaired\" -> \"output_unpaired_peak_summits_file\";\n  \"peak-calling-unpaired\" -> \"output_unpaired_extended_peak_file\";\n  \"peak-calling\" -> \"output_peak_xls_file\";\n  \"count-peaks-unpaired\" -> \"output_unpaired_peak_count_within_replicate\";\n  \"peak-calling-unpaired\" -> \"output_unpaired_peak_xls_file\";\n  \"peaks-bed-to-bigbed\" -> \"output_peak_bigbed_file\";\n  \"spp\" -> \"output_spp_cross_corr_plot\";\n  \"spp\" -> \"output_spp_x_cross_corr\";\n  \"count-reads-filtered-unpaired\" -> \"output_unpaired_filtered_read_count_file\";\n  \"extract-count-reads-in-peaks\" -> \"output_read_in_peak_count_within_replicate\";\n  \"peak-calling\" -> \"output_extended_peak_file\";\n  \"peak-calling\" -> \"output_peak_file\";\n  \"count-reads-filtered\" -> \"output_filtered_read_count_file\";\n  \"peak-calling-unpaired\" -> \"output_unpaired_peak_file\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","visualisationPng":"/graph/png/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","visualisationSvg":"/graph/svg/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","roBundle":"/robundle/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl","licenseName":"MIT License"}