Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
43 lines (41 sloc) 1023 Bytes
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "umi per-lane alignment subworkflow"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
read_structure:
type: string[]
reference: string
outputs:
aligned_bam:
type: File
secondaryFiles: [^.bai]
outputSource: align/aligned_bam
adapter_metrics:
type: File
outputSource: mark_illumina_adapters/metrics
steps:
extract_umis:
run: ../tools/extract_umis.cwl
in:
bam: bam
read_structure: read_structure
out:
[umi_extracted_bam]
mark_illumina_adapters:
run: ../tools/mark_illumina_adapters.cwl
in:
bam: extract_umis/umi_extracted_bam
out:
[marked_bam, metrics]
align:
run: ../tools/umi_align.cwl
in:
bam: mark_illumina_adapters/marked_bam
reference: reference
out:
[aligned_bam]
You can’t perform that action at this time.