#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement - class: ScatterFeatureRequirement - class: SchemaDefRequirement types: - $import: ../../tools/readgroup.yml - class: StepInputExpressionRequirement - class: SubworkflowFeatureRequirement inputs: - id: readgroup_fastq_pe_uuid type: ../../tools/readgroup.yml#readgroup_fastq_pe_uuid - id: bioclient_config type: File outputs: - id: output type: ../../tools/readgroup.yml#readgroup_fastq_pe_file outputSource: emit_readgroup_fastq_pe_file/output steps: - id: extract_forward_fastq run: ../../tools/bio_client_download.cwl in: - id: config-file source: bioclient_config - id: download_handle source: readgroup_fastq_pe_uuid valueFrom: $(self.forward_fastq_uuid) - id: file_size source: readgroup_fastq_pe_uuid valueFrom: $(self.forward_fastq_file_size) out: - id: output - id: extract_reverse_fastq run: ../../tools/bio_client_download.cwl in: - id: config-file source: bioclient_config - id: download_handle source: readgroup_fastq_pe_uuid valueFrom: $(self.reverse_fastq_uuid) - id: file_size source: readgroup_fastq_pe_uuid valueFrom: $(self.reverse_fastq_file_size) out: - id: output - id: emit_readgroup_fastq_pe_file run: ../../tools/emit_readgroup_fastq_pe_file.cwl in: - id: forward_fastq source: extract_forward_fastq/output - id: reverse_fastq source: extract_reverse_fastq/output - id: readgroup_meta source: readgroup_fastq_pe_uuid valueFrom: $(self.readgroup_meta) out: - id: output