subworkflows_sequence_to_bqsr.cwl

Documentation for sequence_to_bqsr.cwl

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Overview

Raw sequence data to BQSR

Inputs

Name	Label	Description	Type	Secondary Files
unaligned			../types/sequence_data.yml#sequence_data[]
bqsr_known_sites		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.	File[]	['.tbi']
bqsr_intervals			string[]?
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
trimming			['../types/trimming_options.yml#trimming_options', 'null']
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/sequence_align_and_tag_adapter.cwl
merge	tools/merge_bams.cwl
name_sort	tools/name_sort.cwl
mark_duplicates_and_sort	tools/mark_duplicates_and_sort.cwl
bqsr	tools/bqsr.cwl
apply_bqsr	tools/apply_bqsr.cwl
index_bam	tools/index_bam.cwl