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#!/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