{"@id":"https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"1a0dd34d59ec983d1f7ad77bff35da2f016e3134","path":"v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl"},"retrievedOn":"2023-01-03T22:40:42.421+00:00","lastCommit":"1a0dd34d59ec983d1f7ad77bff35da2f016e3134","label":"04-peakcall-se.cwl","doc":"ATAC-seq 04 quantification - SE","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_spp_cross_corr_plot":{"doc":"peakshift/phantomPeak results file","type":"File[]"},"output_filtered_read_count_file":{"doc":"Filtered read count reported by MACS2","type":"File[]"},"output_peak_count_within_replicate":{"doc":"Peak counts within replicate","type":"File[]"},"output_read_in_peak_count_within_replicate":{"doc":"Reads peak counts within replicate","type":"File[]"}},"steps":{"spp":{"run":"../spp/spp.cwl","runType":"COMMANDLINETOOL","sources":{"spp":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl#spp/input_bam":{"sourceIDs":["input_bam_files"]}}},"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/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl#peak-calling/treatment":{"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"]}}},"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/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl#peaks-bed-to-bigbed/bed":{"sourceIDs":["trunk-peak-score"]},"https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl#peaks-bed-to-bigbed/genome_sizes":{"sourceIDs":["input_genome_sizes"]}}},"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":["peak-calling"]},"https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl#filter-reads-in-peaks/input_bam_file":{"sourceIDs":["input_bam_files"]}}},"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"]}}},"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"]}}}},"cwltoolVersion":"3.1.20221201130942","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    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