subworkflows_umi_alignment.cwl

Documentation for umi_alignment.cwl

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Overview

umi per-lane alignment subworkflow

Inputs

Name	Label	Description	Type	Secondary Files
bam			File
read_structure			string[]
reference			['string', 'File']	['.amb', '.ann', '.bwt', '.pac', '.sa']

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File	['^.bai']
adapter_metrics			File

Steps

Name	CWL Run
extract_umis	tools/extract_umis.cwl
mark_illumina_adapters	tools/mark_illumina_adapters.cwl
align	tools/umi_align.cwl