Workflow: preprocess_vcf.cwl

Fetched 2019-09-19 10:53:21 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
gather_dkfz_embl_svs
preprocess_vcf.cwl#gather_dkfz_embl_svs/09536f28-65b8-4483-8727-87838fb06529 (ExpressionTool)
gather_broad_snvs
preprocess_vcf.cwl#gather_broad_snvs/b8e36811-aeef-43eb-b906-5fe343f30c27 (ExpressionTool)
gather_sanger_indels
preprocess_vcf.cwl#gather_sanger_indels/111e9f6b-2d3f-4283-b0be-7d68c4df0d7e (ExpressionTool)
gather_sanger_svs
preprocess_vcf.cwl#gather_sanger_svs/d78a5134-5b28-4d5e-aa0b-5f97e56c980a (ExpressionTool)
gather_dkfz_embl_snvs
preprocess_vcf.cwl#gather_dkfz_embl_snvs/c7095dcc-543c-4e28-a237-15b4004dee3e (ExpressionTool)
gather_dkfz_embl_indels
preprocess_vcf.cwl#gather_dkfz_embl_indels/656368d5-6f4b-46d6-b2d3-51cef389c928 (ExpressionTool)
gather_muse_snvs_for_cleaning
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/f390bbd4-ff51-4e87-b030-d571d85708fa (ExpressionTool)
gather_muse_snvs
preprocess_vcf.cwl#gather_muse_snvs/7dff2ccd-b528-4ec1-ac00-a5bf21043f2b (ExpressionTool)
filter_for_indel
preprocess_vcf.cwl#filter_for_indel/f6365ac6-36ac-400e-be22-bdb182d5ee6f (ExpressionTool)
clean_muse
clean_vcf.cwl (CommandLineTool)
clean-vcf

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

clean
clean_vcf.cwl (CommandLineTool)
clean-vcf

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

gather_sanger_snvs
preprocess_vcf.cwl#gather_sanger_snvs/3906044a-c305-41db-bdee-f71b0ec409de (ExpressionTool)
populate_output_record
preprocess_vcf.cwl#populate_output_record/d9bbcddf-2588-4d1a-a23c-1dabff400858 (ExpressionTool)
gather_broad_svs
preprocess_vcf.cwl#gather_broad_svs/fa37e28f-04a8-46c4-863b-7b37f8cef181 (ExpressionTool)
gather_smufin_indels
preprocess_vcf.cwl#gather_smufin_indels/96123cf4-72b6-410d-8b00-83fff157dbcf (ExpressionTool)
extract_snv
extract_snv.cwl (CommandLineTool)
extract_snvs

This tool will extract SNVs from INDEL VCFs

normalize
normalize.cwl (CommandLineTool)
normalize

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

null_filter_extracted_snvs
preprocess_vcf.cwl#null_filter_extracted_snvs/4f73aa99-e8eb-43df-84c4-5ac67e88d2c8 (ExpressionTool)
pass_filter
pass-filter.cwl (CommandLineTool)
pass-filter

This tool will pass-filter a VCF.

merge_vcfs
vcf_merge.cwl (CommandLineTool)
merge_vcfs

This tool will merge VCFs by type (SV, SNV, INDEL). This CWL wrapper was written by Solomon Shorser. The Perl script was originaly written by Brian O'Connor and maintained by Solomon Shorser.

gather_broad_indels
preprocess_vcf.cwl#gather_broad_indels/dda5d245-2e6c-4af1-9a8e-cef9ca46d0ab (ExpressionTool)

Outputs

ID Type Label Doc
preprocessedFiles https://w3id.org/cwl/view/git/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/PreprocessedFilesType.yaml#PreprocessedFileset
Permalink: https://w3id.org/cwl/view/git/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/preprocess_vcf.cwl