subworkflows_align_sort_markdup.cwl

Documentation for align_sort_markdup.cwl

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Overview

Unaligned bam to sorted, markduped bam

Inputs

Name	Label	Description	Type	Secondary Files
bams			File[]
readgroups			string[]
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
final_name			string

Outputs

Name	Label	Description	Type	Secondary Files
final_bam			File	['.bai', '^.bai']
mark_duplicates_metrics_file			File

Steps

Name	CWL Run
align	subworkflows/align.cwl
merge	tools/merge_bams_samtools.cwl
name_sort	tools/name_sort.cwl
mark_duplicates_and_sort	tools/mark_duplicates_and_sort.cwl
index_bam	tools/index_bam.cwl