{"@id":"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","retrievedFrom":{"repoUrl":"https://github.com/Barski-lab/workflows.git","branch":"8587882f145d3eb8e258e7bf819a94f8dd666dbf","path":"workflows/super-enhancer.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/Barski-lab/workflows/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","url":"https://github.com/Barski-lab/workflows/blob/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl"},"retrievedOn":"2026-10-31T13:58:37.918+00:00","lastCommit":"8587882f145d3eb8e258e7bf819a94f8dd666dbf","label":"super-enhancer.cwl","doc":"Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or\nmacs2-callpeak-biowardrobe-only.cwl)\n","inputs":{"bambai_pair":{"label":"Coordinate sorted BAM alignment file (+index BAI)","doc":"Coordinate sorted BAM file and BAI index file","type":"File [BAM]","format":"http://edamontology.org/format_2572"},"promoter_bp":{"label":"Promoter distance","doc":"Promoter distance for gene names assignment","type":"Integer"},"islands_file":{"label":"XLS called peaks file","doc":"XLS file to include information about peaks returned by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl","type":"File [xls]","format":"http://edamontology.org/format_3468"},"tss_distance":{"label":"TSS distance","doc":"Distance from TSS to exclude, 0 = no TSS exclusion","type":"Integer"},"annotation_file":{"label":"Annotation file","doc":"Tab-separated input annotation file","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"stitch_distance":{"label":"Stitching distance","doc":"Linking distance for stitching","type":"Integer"},"chrom_length_file":{"label":"Chromosome length file","doc":"Chromosome length file","type":"File [Textual format]","format":"http://edamontology.org/format_2330"},"islands_control_file":{"label":"XLS called peaks file (control)","doc":"XLS file to include information about peaks returned by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl for control","type":"File (Optional) [xls]","format":"http://edamontology.org/format_3468"}},"outputs":{"png_file":{"label":"ROSE visualization plot","doc":"Generated by ROSE visualization plot","type":"File [PNG]","format":"http://edamontology.org/format_3603"},"bigbed_file":{"label":"Gateway Super Enhancer bigBed file","doc":"Gateway Super Enhancer bigBed file","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"gene_names_file":{"label":"Gateway Super Enhancer results from ROSE with gene names","doc":"Gateway Super Enhancer results from ROSE with assigned gene names","type":"File [TSV]","format":"http://edamontology.org/format_3475"}},"steps":{"make_gff":{"doc":"Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool\nBoth islands_file and islands_control_file should be produced by the same tool\n","run":"../tools/makegff.cwl","runType":"COMMANDLINETOOL","sources":{"make_gff":{"sourceIDs":["islands_file"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#make_gff/islands_control_file":{"sourceIDs":["islands_control_file"]}}},"run_rose":{"doc":"Tool runs ROSE to get Super Enhancers regions\n-b and -c arguments are not supported\n","run":"../tools/rose.cwl","runType":"COMMANDLINETOOL","sources":{"run_rose":{"sourceIDs":["make_gff"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#run_rose/bam_file":{"sourceIDs":["bambai_pair"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#run_rose/tss_distance":{"sourceIDs":["tss_distance"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#run_rose/annotation_file":{"sourceIDs":["annotation_file"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#run_rose/stitch_distance":{"sourceIDs":["stitch_distance"]}}},"sort_bed":{"doc":"Tool sorts data from `unsorted_file` by key\n\n`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.\n","run":"../tools/linux-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort_bed":{"sourceIDs":["run_rose"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#sort_bed/key":{"defaultVal":"\\\"3,3n\\\""}}},"rename_png":{"doc":"Tool renames `source_file` to `target_filename`.\nInput `target_filename` should be set as string. If it's a full path, only basename will be used.\nIf BAI file is present, it will be renamed too\n","run":"../tools/rename.cwl","runType":"COMMANDLINETOOL","sources":{"rename_png":{"sourceIDs":["bambai_pair"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#rename_png/source_file":{"sourceIDs":["run_rose"]}}},"bed_to_macs":{"doc":"Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n","run":"../tools/custom-bash.cwl","runType":"COMMANDLINETOOL","sources":{"bed_to_macs":{"defaultVal":"\\\"cat $0 | grep -v \\\"#\\\" | awk 'BEGIN {print \\\"chr\\tstart\\tend\\tlength\\tabs_summit\\tpileup\\t-log10(pvalue)\\tfold_enrichment\\t-log10(qvalue)\\tname\\\"} {print $1\\\"\\t\\\"$2\\\"\\t\\\"$3\\\"\\t\\\"$3-$2+1\\\"\\t0\\t0\\t0\\t0\\t0\\t\\\"$4}' > `basename $0`\n\\\""},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#bed_to_macs/input_file":{"sourceIDs":["sort_bed"]}}},"assign_genes":{"doc":"Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic)\n\n`default_output_filename` function returns output filename with sufix set as `ext` argument. Function is called when\neither `output_filename` or `log_filename` inputs are not provided.\n","run":"../tools/iaintersect.cwl","runType":"COMMANDLINETOOL","sources":{"assign_genes":{"sourceIDs":["annotation_file"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#assign_genes/promoter_bp":{"sourceIDs":["promoter_bp"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#assign_genes/input_filename":{"sourceIDs":["bed_to_macs"]}}},"bed_to_bigbed":{"doc":"Tool converts bed file to bigBed\n\nBefore running `baseCommand` the following files are created in Docker working directory (using\n`InitialWorkDirRequirement`):\n`narrowpeak.as` - default BED file structure template for ENCODE narrowPeak format\n`broadpeak.as`  - default BED file structure template for ENCODE broadPeak format\n\n`default_output_filename` function returns default output file name based on `input_bed` basename with `*.bb`\nextension if `output_filename` is not provided.\n\n`get_bed_type` function returns default BED file type if `bed_type` is not provided. Depending on `input_bed` file\nextension the following values are returned:\n  `*.narrowpeak`  -->   bed6+4\n  `*.broadpeak`   -->   bed6+3\n   else           -->   null (`bedToBigBed` will use its own default value)\n\n`get_bed_template` function returns default BED file template if `bed_template` is not provided. Depending on\n`input_bed` file extension the following values are returned:\n    `*.narrowpeak`  -->   narrowpeak.as (previously staged into Docker working directory)\n    `*.broadpeak`   -->   broadpeak.as (previously staged into Docker working directory)\n     else           -->   null (`bedToBigBed` will use its own default value)\n","run":"../tools/ucsc-bedtobigbed.cwl","runType":"COMMANDLINETOOL","sources":{"bed_to_bigbed":{"sourceIDs":["chrom_length_file"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#bed_to_bigbed/bed_type":{"defaultVal":"\\\"bed6\\\""},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#bed_to_bigbed/input_bed":{"sourceIDs":["sort_bed"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#bed_to_bigbed/output_filename":{"sourceIDs":["bambai_pair"]}}},"add_island_names":{"doc":"Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n","run":"../tools/custom-bash.cwl","runType":"COMMANDLINETOOL","sources":{"add_island_names":{"defaultVal":"\\\"echo -e \\\"refseq_id\\tgene_id\\ttxStart\\ttxEnd\\tstrand\\tchrom\\tstart\\tend\\tlength\\tregion\\tname\\tscore\\\" > `basename $2`;\ncat $0 | grep -v refseq_id | paste - $1 | cut -f 1-9,15,19,20 >> `basename $2`\n\\\""},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#add_island_names/param":{"sourceIDs":["bambai_pair"]},"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl#add_island_names/input_file":{"sourceIDs":["assign_genes"]}}}},"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    \"islands_file\" [fillcolor=\"#94DDF4\",label=\"XLS called peaks file\"];\n    \"annotation_file\" [fillcolor=\"#94DDF4\",label=\"Annotation file\"];\n    \"chrom_length_file\" [fillcolor=\"#94DDF4\",label=\"Chromosome length file\"];\n    \"tss_distance\" [fillcolor=\"#94DDF4\",label=\"TSS distance\"];\n    \"islands_control_file\" [fillcolor=\"#94DDF4\",label=\"XLS called peaks file (control)\"];\n    \"bambai_pair\" [fillcolor=\"#94DDF4\",label=\"Coordinate sorted BAM alignment file (+index BAI)\"];\n    \"promoter_bp\" [fillcolor=\"#94DDF4\",label=\"Promoter distance\"];\n    \"stitch_distance\" [fillcolor=\"#94DDF4\",label=\"Stitching distance\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"gene_names_file\" [fillcolor=\"#94DDF4\",label=\"Gateway Super Enhancer results from ROSE with gene names\"];\n    \"png_file\" [fillcolor=\"#94DDF4\",label=\"ROSE visualization plot\"];\n    \"bigbed_file\" [fillcolor=\"#94DDF4\",label=\"Gateway Super Enhancer bigBed file\"];\n  }\n  \"add_island_names\" [label=\"add_island_names\"];\n  \"rename_png\" [label=\"rename_png\"];\n  \"bed_to_bigbed\" [label=\"bed_to_bigbed\"];\n  \"sort_bed\" [label=\"sort_bed\"];\n  \"make_gff\" [label=\"make_gff\"];\n  \"bed_to_macs\" [label=\"bed_to_macs\"];\n  \"run_rose\" [label=\"run_rose\"];\n  \"assign_genes\" [label=\"assign_genes\"];\n  \"default1\" -> \"add_island_names\" [label=\"script\"];\n  \"default1\" [label=\"\\\"echo -e \\\"refseq_id\\tgene_id\\ttxStart\\ttxEnd\\tstrand\\tchrom\\tstart\\tend\\tlength\\tregion\\tname\\tscore\\\" > `basename $2`;\ncat $0 | grep -v refseq_id | paste - $1 | cut -f 1-9,15,19,20 >> `basename $2`\n\\\"\", fillcolor=\"#D5AEFC\"];\n  \"bambai_pair\" -> \"add_island_names\" [label=\"param\"];\n  \"sort_bed\" -> \"add_island_names\" [label=\"input_file\"];\n  \"assign_genes\" -> \"add_island_names\" [label=\"input_file\"];\n  \"bambai_pair\" -> \"rename_png\" [label=\"target_filename\"];\n  \"run_rose\" -> \"rename_png\" [label=\"source_file\"];\n  \"chrom_length_file\" -> \"bed_to_bigbed\" [label=\"chrom_length_file\"];\n  \"bambai_pair\" -> \"bed_to_bigbed\" [label=\"output_filename\"];\n  \"sort_bed\" -> \"bed_to_bigbed\" [label=\"input_bed\"];\n  \"default2\" -> \"bed_to_bigbed\" [label=\"bed_type\"];\n  \"default2\" [label=\"\\\"bed6\\\"\", fillcolor=\"#D5AEFC\"];\n  \"run_rose\" -> \"sort_bed\" [label=\"unsorted_file\"];\n  \"default3\" -> \"sort_bed\" [label=\"key\"];\n  \"default3\" [label=\"\\\"2,2n\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default4\" -> \"sort_bed\" [label=\"key\"];\n  \"default4\" [label=\"\\\"1,1\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default5\" -> \"sort_bed\" [label=\"key\"];\n  \"default5\" [label=\"\\\"3,3n\\\"\", fillcolor=\"#D5AEFC\"];\n  \"islands_file\" -> \"make_gff\" [label=\"islands_file\"];\n  \"islands_control_file\" -> \"make_gff\" [label=\"islands_control_file\"];\n  \"default6\" -> \"bed_to_macs\" [label=\"script\"];\n  \"default6\" [label=\"\\\"cat $0 | grep -v \\\"#\\\" | awk 'BEGIN {print \\\"chr\\tstart\\tend\\tlength\\tabs_summit\\tpileup\\t-log10(pvalue)\\tfold_enrichment\\t-log10(qvalue)\\tname\\\"} {print $1\\\"\\t\\\"$2\\\"\\t\\\"$3\\\"\\t\\\"$3-$2+1\\\"\\t0\\t0\\t0\\t0\\t0\\t\\\"$4}' > `basename $0`\n\\\"\", fillcolor=\"#D5AEFC\"];\n  \"sort_bed\" -> \"bed_to_macs\" [label=\"input_file\"];\n  \"make_gff\" -> \"run_rose\" [label=\"binding_sites_file\"];\n  \"bambai_pair\" -> \"run_rose\" [label=\"bam_file\"];\n  \"stitch_distance\" -> \"run_rose\" [label=\"stitch_distance\"];\n  \"annotation_file\" -> \"run_rose\" [label=\"annotation_file\"];\n  \"tss_distance\" -> \"run_rose\" [label=\"tss_distance\"];\n  \"annotation_file\" -> \"assign_genes\" [label=\"annotation_filename\"];\n  \"bed_to_macs\" -> \"assign_genes\" [label=\"input_filename\"];\n  \"promoter_bp\" -> \"assign_genes\" [label=\"promoter_bp\"];\n  \"add_island_names\" -> \"gene_names_file\";\n  \"rename_png\" -> \"png_file\";\n  \"bed_to_bigbed\" -> \"bigbed_file\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/Barski-lab/workflows/blob/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","visualisationPng":"/graph/png/github.com/Barski-lab/workflows/blob/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","visualisationSvg":"/graph/svg/github.com/Barski-lab/workflows/blob/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","roBundle":"/robundle/github.com/Barski-lab/workflows/blob/8587882f145d3eb8e258e7bf819a94f8dd666dbf/workflows/super-enhancer.cwl","licenseName":"Apache License 2.0"}