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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: File
secondaryFiles: [.fai, .bwt, .sa, .ann, .amb, .pac, .alt]
readgroup:
type: string
outputs:
tagged_bam:
type: File
outputSource: align_and_tag/aligned_bam
steps:
revert_to_fastq:
run: revert_to_fastq.cwl
in:
bam: bam
out:
[fastq, second_end_fastq]
align_and_tag:
run: align_and_tag.cwl
in:
in:
readgroup: readgroup
reference: reference
fastq: revert_to_fastq/fastq
fastq2: revert_to_fastq/second_end_fastq
out:
[aligned_bam]
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