#!/usr/bin/env cwl-runner cwlVersion: v1.0 requirements: - class: InlineJavascriptRequirement - class: ScatterFeatureRequirement - class: SchemaDefRequirement types: - $import: ../../tools/readgroup.yml class: Workflow inputs: - id: input type: ../../tools/readgroup.yml#readgroup_fastq_pe_file - id: job_uuid type: string outputs: - id: output type: ../../tools/readgroup.yml#readgroup_fastq_pe_file outputSource: emit_readgroup_fastq_pe_file/output - id: sqlite type: File outputSource: json_to_sqlite/sqlite steps: - id: fastq_cleaner_pe run: ../../tools/fastq_cleaner_pe.cwl in: - id: fastq1 source: input valueFrom: $(self.forward_fastq) - id: fastq2 source: input valueFrom: $(self.reverse_fastq) out: - id: cleaned_fastq1 - id: cleaned_fastq2 - id: result_json - id: emit_readgroup_fastq_pe_file run: ../../tools/emit_readgroup_fastq_pe_file.cwl in: - id: forward_fastq source: fastq_cleaner_pe/cleaned_fastq1 - id: reverse_fastq source: fastq_cleaner_pe/cleaned_fastq2 - id: readgroup_meta source: input valueFrom: $(self.readgroup_meta) out: - id: output - id: json_to_sqlite run: ../../tools/json_to_sqlite.cwl in: - id: input_json source: fastq_cleaner_pe/result_json - id: job_uuid source: job_uuid - id: table_name valueFrom: "fastq_cleaner_pe" out: - id: sqlite - id: log