Documentation for manta_somatic.cwl

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Overview

Set up and execute manta

Docker Requirement

mgibio/manta_somatic-cwl:1.6.0

Inputs

Name	Label	Description	Type	Secondary Files
normal_bam			File?	${if (self.nameext === ".bam") {return self.basename + ".bai"} else {return self.basename + ".crai"}}
tumor_bam			File	${if (self.nameext === ".bam") {return self.basename + ".bai"} else {return self.basename + ".crai"}}
reference			['string', 'File']	['.fai', '^.dict']
call_regions		bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted	File?	['.tbi']
non_wgs		toggles on settings for WES	boolean?
output_contigs		if true, outputs assembled contig sequences in final VCF files, in the INFO field CONTIG	boolean?

Outputs

Name	Label	Description	Type	Secondary Files
diploid_variants			File?	['.tbi']
somatic_variants			File?	['.tbi']
all_candidates			File	['.tbi']
small_candidates			File	['.tbi']
tumor_only_variants			File?	['.tbi']