#!/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: bioclient_config type: File - id: readgroups_bam_uuid type: ../../tools/readgroup.yml#readgroups_bam_uuid outputs: - id: output type: ../../tools/readgroup.yml#readgroups_bam_file outputSource: emit_readgroups_bam_file/output steps: - id: extract_bam run: ../../tools/bio_client_download.cwl in: - id: config-file source: bioclient_config - id: download_handle source: readgroups_bam_uuid valueFrom: $(self.bam_uuid) - id: file_size source: readgroups_bam_uuid valueFrom: $(self.bam_file_size) out: - id: output - id: emit_readgroups_bam_file run: ../../tools/emit_readgroups_bam_file.cwl in: - id: bam source: extract_bam/output - id: readgroup_meta_list source: readgroups_bam_uuid valueFrom: $(self.readgroup_meta_list) out: - id: output