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sequence_align_and_tag_adapter.cwl
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sequence_align_and_tag_adapter.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "adapter for sequence_align_and_tag"
doc: "Some workflow engines won't stage files in our nested structure, so parse it out here"
requirements:
- class: InlineJavascriptRequirement
- class: SchemaDefRequirement
types:
- $import: ../types/sequence_data.yml
- $import: ../types/trimming_options.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
unaligned:
type: ../types/sequence_data.yml#sequence_data
doc: "the unaligned sequence data with readgroup information"
reference:
type:
- string
- File
secondaryFiles: [.amb, .ann, .bwt, .pac, .sa]
doc: 'bwa-indexed reference file'
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
outputs:
aligned_bam:
type: File
outputSource: align_and_tag/aligned_bam
steps:
align_and_tag:
run: ../tools/sequence_align_and_tag.cwl
in:
reference: reference
bam:
source: unaligned
valueFrom: "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)"
fastq1:
source: unaligned
valueFrom: "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)"
fastq2:
source: unaligned
valueFrom: "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)"
readgroup:
source: unaligned
valueFrom: $(self.readgroup)
trimming: trimming
out:
[aligned_bam]