tools_manta_somatic.cwl
Travis CI User edited this page Jan 13, 2021
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Set up and execute manta
mgibio/manta_somatic-cwl:1.6.0
| 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? |
| 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'] |