subworkflows_sequence_align_and_tag_adapter.cwl

Documentation for sequence_align_and_tag_adapter.cwl

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Overview

adapter for sequence_align_and_tag

Introduction

Some workflow engines won't stage files in our nested structure, so parse it out here

Inputs

Name	Label	Description	Type	Secondary Files
unaligned		the unaligned sequence data with readgroup information	../types/sequence_data.yml#sequence_data
reference		bwa-indexed reference file	['string', 'File']	['.amb', '.ann', '.bwt', '.pac', '.sa']
trimming			['../types/trimming_options.yml#trimming_options', 'null']

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File

Steps

Name	CWL Run
align_and_tag	tools/sequence_align_and_tag.cwl