Workflow: mc3_vcf_postfilter.cwl

Fetched 2020-01-29 14:44:21 GMT
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Inputs

ID Type Title Doc
reference File
normal File
rawRadia File
rawPindel File
tumorID String
rawSomsniper File
tumor File
rawIndelocator File
normalID String
rawMuse File
rawVarscans File

Steps

ID Runs Label Doc
filterPindel
tools/vcf-tools/filter_vcf.cwl (CommandLineTool)
Merge VCFs
filterRadia
tools/radia-tool/radia_filter.cwl (CommandLineTool)
RADIA-Filter

Filter radia output. If the input is from exomes plus RNA-Seq, set dnaOnly to False

fpfilterSomaticSniper
tools/fpfilter-tool/fpfilter.cwl.yaml (CommandLineTool)
fpfilter
filterMuse
tools/muse-tool/muse.filter.cwl (CommandLineTool)
Filter MuSE
fpfilterVarscans
tools/fpfilter-tool/fpfilter.cwl.yaml (CommandLineTool)
fpfilter
filterIndelocator
tools/vcf-tools/filter_vcf.cwl (CommandLineTool)
Merge VCFs

Outputs

ID Type Label Doc
filteredMuseVCF File
filteredPindelVCF File
filteredRadiaVCF File
fpfilteredVarscansVCF File
filteredIndelocatorVCF File
fpfilteredSomaticsniperVCF File
Permalink: https://w3id.org/cwl/view/git/a094d41f6fb56c7f8e0acac42f8eb8e36977d92d/mc3_vcf_postfilter.cwl