#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 doc: 'RNA-seq 01 QC - reads: SE' requirements: - class: ScatterFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement inputs: input_fastq_read1_files: doc: Input read1 fastq files type: File[] default_adapters_file: doc: Adapters file type: File nthreads: doc: Number of threads. type: int outputs: output_custom_adapters_read1: outputSource: overrepresented_sequence_extract_read1/output_custom_adapters type: File[] output_fastqc_data_files_read1: doc: FastQC data files for paired read 1 type: File[] outputSource: extract_fastqc_data_read1/output_fastqc_data_file output_count_raw_reads_read1: outputSource: count_raw_reads_read1/output_read_count type: File[] output_fastqc_report_files_read1: doc: FastQC reports in zip format for paired read 1 type: File[] outputSource: fastqc_read1/output_qc_report_file output_diff_counts_read1: outputSource: compare_read_counts_read1/result type: File[] steps: extract_basename_read1: run: ../utils/basename.cwl scatter: file_path in: file_path: source: input_fastq_read1_files valueFrom: $(self.basename) sep: valueFrom: '(\.fastq.gz|\.fastq)' do_not_escape_sep: valueFrom: ${return true} out: - basename count_raw_reads_read1: run: ../utils/count-fastq-reads.cwl scatterMethod: dotproduct scatter: - input_fastq_file - input_basename in: input_basename: extract_basename_read1/basename input_fastq_file: input_fastq_read1_files out: - output_read_count fastqc_read1: run: ../qc/fastqc.cwl scatter: input_fastq_file in: threads: nthreads input_fastq_file: input_fastq_read1_files out: - output_qc_report_file count_fastqc_reads_read1: run: ../qc/count-fastqc-reads.cwl scatterMethod: dotproduct scatter: - input_fastqc_data - input_basename in: input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file input_basename: extract_basename_read1/basename out: - output_fastqc_read_count extract_fastqc_data_read1: run: ../qc/extract_fastqc_data.cwl scatterMethod: dotproduct scatter: - input_qc_report_file - input_basename in: input_basename: extract_basename_read1/basename input_qc_report_file: fastqc_read1/output_qc_report_file out: - output_fastqc_data_file overrepresented_sequence_extract_read1: run: ../qc/overrepresented_sequence_extract.cwl scatterMethod: dotproduct scatter: - input_fastqc_data - input_basename in: input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file input_basename: extract_basename_read1/basename default_adapters_file: default_adapters_file out: - output_custom_adapters compare_read_counts_read1: run: ../qc/diff.cwl scatterMethod: dotproduct scatter: - file1 - file2 in: file2: count_fastqc_reads_read1/output_fastqc_read_count file1: count_raw_reads_read1/output_read_count out: - result