Workflow: preprocess_vcf.cwl

Fetched 2018-12-14 18:14:49 GMT

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

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Inputs

ID Type Title Doc
ref File

Reference file, used for normalized INDELs

out_dir String

The name of the output directory

filesToPreprocess String[]

The files to process

vcfdir Directory

The directory where the files are

Steps

ID Runs Label Doc
populate_output_record
preprocess_vcf.cwl#populate_output_record/f1736d6c-fcc5-40db-80bf-76df2de0a435 (ExpressionTool)
normalize
normalize.cwl (CommandLineTool)
normalize

This tool will normalize an INDEL VCF using bcf-tools norm.

pass_filter
pass-filter.cwl (CommandLineTool)
pass-filter

This tool will pass-filter a VCF.

filter_for_indel
preprocess_vcf.cwl#filter_for_indel/a089287b-da9a-41d3-8e96-42f61c9d2382 (ExpressionTool)
clean
clean_vcf.cwl (CommandLineTool)
clean-vcf

This tool will clean a VCF for use in the OxoG workflow.

Outputs

ID Type Label Doc
preprocessedFiles https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/PreprocessedFilesType.yaml#PreprocessedFileset
Permalink: https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/preprocess_vcf.cwl