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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/capture_kit.yml
inputs:
- id: bioclient_config
type: File
- id: capture_kit_set_uuid
type: ../../tools/capture_kit.yml#capture_kit_set_uuid
outputs:
- id: output
type: ../../tools/capture_kit.yml#capture_kit_set_file
outputSource: emit_capture_kit/output
steps:
- id: extract_capture_kit_bait
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: capture_kit_set_uuid
valueFrom: $(self.capture_kit_bait_uuid)
out:
- id: output
- id: extract_capture_kit_target
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: capture_kit_set_uuid
valueFrom: $(self.capture_kit_target_uuid)
out:
- id: output
- id: emit_capture_kit
run: ../../tools/emit_capture_kit_file.cwl
in:
- id: capture_kit_bait_file
source: extract_capture_kit_bait/output
- id: capture_kit_target_file
source: extract_capture_kit_target/output
out:
- id: output
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