subworkflows_molecular_alignment.cwl

Documentation for molecular_alignment.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', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
target_intervals			File?
min_reads			int[]
max_read_error_rate			float?
max_base_error_rate			float?
min_base_quality			int
max_no_call_fraction			float

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File	['.bai', '^.bai']
adapter_histogram			File[]
duplex_seq_metrics			File[]

Steps

Name	CWL Run
align	subworkflows/umi_alignment.cwl
merge	tools/merge_bams.cwl
group_reads_by_umi	tools/group_reads.cwl
call_molecular_consensus	tools/call_molecular_consensus.cwl
align_consensus	tools/realign.cwl
filter_consensus	tools/filter_consensus.cwl
clip_overlap	tools/clip_overlap.cwl
collect_duplex_seq_metrics	tools/duplex_seq_metrics.cwl
index_bam	tools/index_bam.cwl