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align.cwl
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align.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: 'Unaligned to aligned BAM'
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
bam:
type: File
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
readgroup:
type: string
outputs:
tagged_bam:
type: File
outputSource: align_and_tag/aligned_bam
steps:
align_and_tag:
run: ../tools/align_and_tag.cwl
in:
bam: bam
readgroup: readgroup
reference: reference
out:
[aligned_bam]