Skip to content

subworkflows_qc_exome_no_verify_bam.cwl

Travis CI User edited this page Feb 24, 2021 · 20 revisions

Documentation for qc_exome_no_verify_bam.cwl

This page is auto-generated. Do not edit.

Overview

Exome QC workflow

Inputs

Name Label Description Type Secondary Files
bam File ['^.bai']
reference ['string', 'File'] ['.fai', '^.dict']
bait_intervals File
target_intervals File
picard_metric_accumulation_level string
minimum_mapping_quality int?
minimum_base_quality int?
per_base_intervals ../types/labelled_file.yml#labelled_file[]
per_target_intervals ../types/labelled_file.yml#labelled_file[]
summary_intervals ../types/labelled_file.yml#labelled_file[]

Outputs

Name Label Description Type Secondary Files
insert_size_metrics File
insert_size_histogram File
alignment_summary_metrics File
hs_metrics File
per_target_coverage_metrics File[]
per_target_hs_metrics File[]
per_base_coverage_metrics File[]
per_base_hs_metrics File[]
summary_hs_metrics File[]
flagstats File

Steps

Name CWL Run
collect_insert_size_metrics tools/collect_insert_size_metrics.cwl
collect_alignment_summary_metrics tools/collect_alignment_summary_metrics.cwl
collect_roi_hs_metrics tools/collect_hs_metrics.cwl
collect_detailed_hs_metrics subworkflows/hs_metrics.cwl
samtools_flagstat tools/samtools_flagstat.cwl
Clone this wiki locally