{"@id":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"81555a89cc2d16bd3ab131a6685a44b44f08f927","path":"v1.0/ATAC-seq_pipeline/02-trim-se.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl"},"retrievedOn":"2026-09-25T06:59:16.983+00:00","lastCommit":"81555a89cc2d16bd3ab131a6685a44b44f08f927","label":"02-trim-se.cwl","doc":"ATAC-seq 02 trimming - reads: SE","inputs":{"nthreads":{"doc":"Number of threads","type":"Integer"},"quality_score":{"type":"String"},"input_fastq_files":{"doc":"Input fastq files","type":"File[]"},"input_adapters_files":{"doc":"Input adapters files","type":"File[]"},"trimmomatic_jar_path":{"doc":"Trimmomatic Java jar file","type":"String"},"trimmomatic_java_opts":{"doc":"JVM arguments should be a quoted, space separated list","type":"String (Optional)"}},"outputs":{"output_data_fastq_trimmed_files":{"doc":"Trimmed fastq files","type":"File[]"},"output_trimmed_fastq_read_count":{"doc":"Trimmed read counts of fastq files","type":"File[]"}},"steps":{"trimmomatic":{"doc":"Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop\nIllumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem\ndepending on the library preparation and downstream application.\nThere are two major modes of the program: Paired end mode and Single end mode. The\npaired end mode will maintain correspondence of read pairs and also use the additional\ninformation contained in paired reads to better find adapter or PCR primer fragments\nintroduced by the library preparation process.\nTrimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores,\ndepending on the Illumina pipeline used).\n","run":"../trimmomatic/trimmomatic.cwl","runType":"COMMANDLINETOOL","sources":{"trimmomatic":{"sourceIDs":["input_fastq_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl#trimmomatic/nthreads":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl#trimmomatic/java_opts":{"sourceIDs":["trimmomatic_java_opts"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl#trimmomatic/input_adapters_file":{"sourceIDs":["input_adapters_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl#trimmomatic/trimmomatic_jar_path":{"sourceIDs":["trimmomatic_jar_path"]}}},"extract_basename":{"doc":"Extracts the base name of a file","run":"../utils/extract-basename.cwl","runType":"COMMANDLINETOOL","sources":{"extract_basename":{"sourceIDs":["trimmomatic"]}}},"count_fastq_reads":{"doc":"Counts reads in a fastq file","run":"../utils/count-fastq-reads.cwl","runType":"COMMANDLINETOOL","sources":{"count_fastq_reads":{"sourceIDs":["trimmomatic"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl#count_fastq_reads/input_basename":{"sourceIDs":["extract_basename"]}}}},"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    \"trimmomatic_jar_path\" [fillcolor=\"#94DDF4\",label=\"trimmomatic_jar_path\"];\n    \"input_fastq_files\" [fillcolor=\"#94DDF4\",label=\"input_fastq_files\"];\n    \"input_adapters_files\" [fillcolor=\"#94DDF4\",label=\"input_adapters_files\"];\n    \"nthreads\" [fillcolor=\"#94DDF4\",label=\"nthreads\"];\n    \"trimmomatic_java_opts\" [fillcolor=\"#94DDF4\",label=\"trimmomatic_java_opts\"];\n    \"quality_score\" [fillcolor=\"#94DDF4\",label=\"quality_score\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"output_data_fastq_trimmed_files\" [fillcolor=\"#94DDF4\",label=\"output_data_fastq_trimmed_files\"];\n    \"output_trimmed_fastq_read_count\" [fillcolor=\"#94DDF4\",label=\"output_trimmed_fastq_read_count\"];\n  }\n  \"count_fastq_reads\" [label=\"count_fastq_reads\"];\n  \"extract_basename\" [label=\"extract_basename\"];\n  \"trimmomatic\" [label=\"trimmomatic\"];\n  \"trimmomatic\" -> \"count_fastq_reads\" [label=\"input_fastq_file\"];\n  \"extract_basename\" -> \"count_fastq_reads\" [label=\"input_basename\"];\n  \"trimmomatic\" -> \"extract_basename\" [label=\"input_file\"];\n  \"input_fastq_files\" -> \"trimmomatic\" [label=\"input_read1_fastq_file\"];\n  \"input_adapters_files\" -> \"trimmomatic\" [label=\"input_adapters_file\"];\n  \"nthreads\" -> \"trimmomatic\" [label=\"nthreads\"];\n  \"trimmomatic_java_opts\" -> \"trimmomatic\" [label=\"java_opts\"];\n  \"trimmomatic_jar_path\" -> \"trimmomatic\" [label=\"trimmomatic_jar_path\"];\n  \"trimmomatic\" -> \"output_data_fastq_trimmed_files\";\n  \"count_fastq_reads\" -> \"output_trimmed_fastq_read_count\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","visualisationPng":"/graph/png/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","visualisationSvg":"/graph/svg/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","roBundle":"/robundle/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/02-trim-se.cwl","licenseName":"MIT License"}