{"@id":"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","retrievedFrom":{"repoUrl":"https://github.com/CompEpigen/ChIPseq_workflows.git","branch":"e2f3e99deba204a31af06646a8326b41242b07a8","path":"CWL/workflows/CUTnRUN.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/CompEpigen/ChIPseq_workflows/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","url":"https://github.com/CompEpigen/ChIPseq_workflows/blob/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl"},"retrievedOn":"2026-09-26T18:02:50.166+00:00","lastCommit":"e2f3e99deba204a31af06646a8326b41242b07a8","label":"CUTnRUN.cwl","inputs":{"fastq1":{"doc":"List of fastq files containing the first mate of raw reads. \nMuliple files are provided if  multiplexing of the same library has been done \non multiple lanes. The reads comming from different fastq files are pooled \nafter alignment. Also see parameter \\\"fastq2\\\". \n","type":"File[]"},"fastq2":{"doc":"List of fastq files containing the second mate of raw reads in case of paired end \n(also see parameter \\\"fastq1\\\"). \nImportant: this list has to be of same length as parameter \\\"fastq1\\\" no matter if paired or single end is used. \nIn case of single end data specify \\\"null\\\" for every entry of fastq1. \n","type":"File[]"},"genome":{"doc":"Path to reference genome in fasta format. \nBowtie2 index files (\\\".1.bt2\\\", \\\".2.bt2\\\", ...) as well as a samtools index (\\\".fai\\\") \nhas to be located in the same directory.\\n\nAll of these files can be downloaded for the most common genome builds at  \nhttps://support.illumina.com/sequencing/sequencing_software/igenome.html. \nAlternatively, you can use \\\"bowtie2-build\\\" or \\\"samtools index\\\" to create them yourself.\n","type":"File"},"adapter1":{"doc":"Adapter sequence for first reads. \nIf not specified (set to \\\"null\\\"), trim_galore will try to autodetect whether ...\\n\n- Illumina universal adapter (AGATCGGAAGAGC)\\n\n- Nextera adapter (CTGTCTCTTATA)\\n\n- Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\\n\n... was used.\\n\nYou can directly choose one of the above configurations \nby setting the string to \\\"illumina\\\", \\\"nextera\\\", or \\\"small_rna\\\". \nOr you specify the adaptor string manually (e.g. \\\"AGATCGGAAGAGC\\\").\n","type":"String (Optional)"},"adapter2":{"doc":"Adapter sequence for second reads (only relevant for paired end data). \nIf it is not specified (set to \\\"null\\\"), trim_galore will try to autodetect whether ...\\n\n- Illumina universal adapter (AGATCGGAAGAGC)\\n\n- Nextera adapter (CTGTCTCTTATA)\\n\n- Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\\n\n... was used.\\n\nYou can directly choose one of the above configurations \nby setting the string to \\\"illumina\\\", \\\"nextera\\\", or \\\"small_rna\\\". \nOr you specify the adaptor string manually (e.g. \\\"AGATCGGAAGAGC\\\").\n","type":"String (Optional)"},"bin_size":{"doc":"Bin size used for generation of coverage tracks. \nThe larger the bin size the smaller are the coverage tracks, however, \nthe less precise is the signal. For single bp resolution set to 1.\n","type":"Integer"},"sample_id":{"doc":"Sample ID used for naming the output files.\n","type":"String"},"fragment_size":{"doc":"Mean library fragment size, used to reconstruct entire \nfragments from single end reads. Not relevant in case of paired end data.\n","type":"Integer (Optional)"},"is_paired_end":{"doc":"If paired end data is used set to true, else set to false.\n","type":"Boolean"},"genome_spike_in":{"doc":"Path to reference genome of the spike-in organism in fasta format. \nBowtie2 index files (\\\".1.bt2\\\", \\\".2.bt2\\\", ...) as well as a samtools index (\\\".fai\\\") \nhas to be located in the same directory.\\n\nAll of these files can be downloaded for the most common genome builds at  \nhttps://support.illumina.com/sequencing/sequencing_software/igenome.html. \nAlternatively, you can use \\\"bowtie2-build\\\" or \\\"samtools index\\\" to create them yourself.\n","type":"File"},"effective_genome_size":{"doc":"The effectively mappable genome size, please see: \nhttps://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html\n","type":"Long"},"ignoreForNormalization":{"doc":"List of space-delimited chromosome names that shall be ignored \nwhen calculating the scaling factor. \nSpecify as space-delimited string. \nDefault: \\\"chrX chrY chrM\\\"\nSpecify as space-delimited string. \nDefault: \\\"chrX chrY chrM\\\"\n","type":"String (Optional)"}},"outputs":{"bam":{"type":"File"},"bigwig":{"type":"File"},"fastqc_zip":{"type":"File[]"},"bowtie2_log":{"type":"File[]"},"fastqc_html":{"type":"File[]"},"multiqc_zip":{"type":"File"},"bam_spike_in":{"type":"File"},"multiqc_html":{"type":"File"},"raw_fastqc_zip":{"type":"0178ffe2c6ebbc90b588a1b61ba25b51[]"},"raw_fastqc_html":{"type":"8db8e8ccc8d2c086021042b04a07e846[]"},"spike_in_counts":{"type":"File"},"trim_galore_log":{"type":"838f9d84f8da44749f1befaf8ac39c76[]"},"qc_crosscorr_plot":{"type":"File (Optional)"},"trimmed_fastqc_zip":{"type":"eb7cdb99dab560ce78d01c2f8af5b58f[]"},"trimmed_fastqc_html":{"type":"392a86caf4a6ab99517c3d961c51d9be[]"},"qc_crosscorr_summary":{"type":"File (Optional)"},"qc_plot_coverage_tsv":{"type":"File"},"qc_plot_coverage_plot":{"type":"File"},"qc_plot_fingerprint_tsv":{"type":"File (Optional)"},"qc_plot_fingerprint_plot":{"type":"File (Optional)"},"qc_plot_fingerprint_stderr":{"type":"File"},"qc_phantompeakqualtools_stderr":{"type":"File (Optional)"}},"steps":{"chip_qc":{"run":"../workflow_modules/chip_qc.cwl","runType":"WORKFLOW","sources":{"chip_qc":{"sourceIDs":["is_paired_end"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#chip_qc/bam":{"sourceIDs":["merge_filter"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#chip_qc/sample_id":{"sourceIDs":["sample_id"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#chip_qc/user_def_fragment_size":{"sourceIDs":["fragment_size"]}}},"merge_filter":{"run":"../workflow_modules/merge_filter.cwl","runType":"WORKFLOW","sources":{"merge_filter":{"sourceIDs":["is_paired_end"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#merge_filter/bams":{"sourceIDs":["trim_and_map"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#merge_filter/sample_id":{"sourceIDs":["sample_id"]}}},"trim_and_map":{"run":"../workflow_modules/trim_and_map.cwl","runType":"WORKFLOW","sources":{"trim_and_map":{"sourceIDs":["adapter1"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#trim_and_map/fastq1":{"sourceIDs":["fastq1"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#trim_and_map/fastq2":{"sourceIDs":["fastq2"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#trim_and_map/genome":{"sourceIDs":["genome"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#trim_and_map/adapter2":{"sourceIDs":["adapter2"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#trim_and_map/is_paired_end":{"sourceIDs":["is_paired_end"]}}},"get_spike_in_counts":{"run":"../workflow_modules/get_spike_in_counts.cwl","runType":"WORKFLOW","sources":{"get_spike_in_counts":{"sourceIDs":["sample_id"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#get_spike_in_counts/is_paired_end":{"sourceIDs":["is_paired_end"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#get_spike_in_counts/fastq1_trimmed":{"sourceIDs":["trim_and_map"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#get_spike_in_counts/fastq2_trimmed":{"sourceIDs":["trim_and_map"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#get_spike_in_counts/genome_spike_in":{"sourceIDs":["genome_spike_in"]}}},"create_summary_qc_report":{"run":"../tools/multiqc_hack.cwl","runType":"COMMANDLINETOOL","sources":{"create_summary_qc_report":{"sourceIDs":["chip_qc"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#create_summary_qc_report/report_name":{"sourceIDs":["sample_id"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#create_summary_qc_report/qc_files_array":{"sourceIDs":["chip_qc"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#create_summary_qc_report/qc_files_array_of_array":{"sourceIDs":["trim_and_map"]}}},"generate_coverage_tracks":{"run":"../tools/deeptools_bamCoverage.cwl","runType":"COMMANDLINETOOL","sources":{"generate_coverage_tracks":{"sourceIDs":["ignoreForNormalization"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/bam":{"sourceIDs":["merge_filter"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/bin_size":{"sourceIDs":["bin_size"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/fragment_size":{"sourceIDs":["chip_qc"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/is_paired_end":{"sourceIDs":["is_paired_end"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/spike_in_count":{"sourceIDs":["get_spike_in_counts"]},"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl#generate_coverage_tracks/effective_genome_size":{"sourceIDs":["effective_genome_size"]}}}},"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    \"ignoreForNormalization\" [fillcolor=\"#94DDF4\",label=\"ignoreForNormalization\"];\n    \"is_paired_end\" [fillcolor=\"#94DDF4\",label=\"is_paired_end\"];\n    \"sample_id\" [fillcolor=\"#94DDF4\",label=\"sample_id\"];\n    \"effective_genome_size\" 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[label=\"sample_id\"];\n  \"is_paired_end\" -> \"get_spike_in_counts\" [label=\"is_paired_end\"];\n  \"genome_spike_in\" -> \"get_spike_in_counts\" [label=\"genome_spike_in\"];\n  \"trim_and_map\" -> \"get_spike_in_counts\" [label=\"fastq2_trimmed\"];\n  \"trim_and_map\" -> \"get_spike_in_counts\" [label=\"fastq1_trimmed\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"merge_filter\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"merge_filter\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"chip_qc\" -> \"create_summary_qc_report\" [label=\"qc_files_array\"];\n  \"trim_and_map\" -> \"create_summary_qc_report\" 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\"bowtie2_log\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/CompEpigen/ChIPseq_workflows/blob/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","visualisationPng":"/graph/png/github.com/CompEpigen/ChIPseq_workflows/blob/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","visualisationSvg":"/graph/svg/github.com/CompEpigen/ChIPseq_workflows/blob/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","roBundle":"/robundle/github.com/CompEpigen/ChIPseq_workflows/blob/e2f3e99deba204a31af06646a8326b41242b07a8/CWL/workflows/CUTnRUN.cwl","licenseName":"Apache License 2.0"}