#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 doc: 'ChIP-seq 02 trimming - reads: SE' requirements: - class: ScatterFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement inputs: input_read1_fastq_files: doc: Input fastq files type: File[] input_adapters_files: doc: Input adapters files type: File[] nthreads: default: 1 doc: Number of threads type: int quality_score: default: -phred33 type: string trimmomatic_java_opts: doc: JVM arguments should be a quoted, space separated list type: string? trimmomatic_jar_path: default: /usr/share/java/trimmomatic.jar doc: Trimmomatic Java jar file type: string steps: extract_basename: run: ../utils/basename.cwl scatter: file_path in: file_path: source: trimmomatic/output_read1_trimmed_file valueFrom: $(self.basename) sep: valueFrom: '(\.fastq.gz|\.fastq)' do_not_escape_sep: valueFrom: ${return true} out: - basename count_fastq_reads: run: ../utils/count-fastq-reads.cwl scatterMethod: dotproduct scatter: - input_fastq_file - input_basename in: input_basename: extract_basename/basename input_fastq_file: trimmomatic/output_read1_trimmed_file out: - output_read_count trimmomatic: run: ../trimmomatic/trimmomatic.cwl scatterMethod: dotproduct scatter: - input_read1_fastq_file - input_adapters_file in: phred: valueFrom: '33' nthreads: nthreads minlen: valueFrom: ${return 15} java_opts: trimmomatic_java_opts leading: valueFrom: ${return 3} slidingwindow: valueFrom: 4:20 illuminaclip: valueFrom: 2:30:15 input_read1_fastq_file: input_read1_fastq_files input_adapters_file: input_adapters_files trailing: valueFrom: ${return 3} trimmomatic_jar_path: trimmomatic_jar_path end_mode: valueFrom: SE out: - output_read1_trimmed_file outputs: output_data_fastq_trimmed_files: doc: Trimmed fastq files type: File[] outputSource: trimmomatic/output_read1_trimmed_file output_trimmed_fastq_read_count: doc: Trimmed read counts of fastq files type: File[] outputSource: count_fastq_reads/output_read_count