subworkflows_molecular_qc.cwl

Documentation for molecular_qc.cwl

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Overview

umi molecular alignment workflow

Inputs

Name	Label	Description	Type	Secondary Files
bam			File[]
sample_name			string
read_structure			string[]
reference			string
target_intervals			File
bait_intervals			File
omni_vcf			File	['.tbi']
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
aligned_bam			File	['.bai', '^.bai']
adapter_histogram			File[]
duplex_seq_metrics			File[]
insert_size_histogram			File
insert_size_metrics			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
verify_bam_id_metrics			File
verify_bam_id_depth			File

Steps

Name	CWL Run
alignment	subworkflows/molecular_alignment.cwl
qc	subworkflows/qc_exome.cwl