Workflow: preprocess_vcf.cwl

Fetched 2023-01-04 23:46:08 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

vcfdir Directory

The directory where the files are

out_dir String

The name of the output directory

filesToPreprocess String[]

The files to process

Steps

ID Runs Label Doc
filter_for_indel
preprocess_vcf.cwl#filter_for_indel/374d0ee7-38cb-430e-8c57-f30cf4dee675 (ExpressionTool)
gather_broad_svs
preprocess_vcf.cwl#gather_broad_svs/6234eaa7-9753-42bb-98b7-6c7584d95330 (ExpressionTool)
gather_muse_snvs
preprocess_vcf.cwl#gather_muse_snvs/4f39ba5c-09e9-4a03-bb99-4afce94e5607 (ExpressionTool)
gather_broad_snvs
preprocess_vcf.cwl#gather_broad_snvs/e9ea7170-9f3c-441d-a1e1-491a263361b4 (ExpressionTool)
gather_sanger_svs
preprocess_vcf.cwl#gather_sanger_svs/65cb870a-cb9d-41d2-b452-9f02069d682a (ExpressionTool)
gather_sanger_snvs
preprocess_vcf.cwl#gather_sanger_snvs/915475cd-2a9a-4e83-ae76-d487dd5a810e (ExpressionTool)
gather_broad_indels
preprocess_vcf.cwl#gather_broad_indels/e6f3a02e-d953-4354-8277-affb3d09be47 (ExpressionTool)
gather_dkfz_embl_svs
preprocess_vcf.cwl#gather_dkfz_embl_svs/93974873-e885-47b3-b1fb-8f9644bf3b8f (ExpressionTool)
gather_sanger_indels
preprocess_vcf.cwl#gather_sanger_indels/912886ff-0e82-45ba-80b0-4bd609467864 (ExpressionTool)
gather_smufin_indels
preprocess_vcf.cwl#gather_smufin_indels/e633cc4a-1a96-4c86-95f5-6fd265f7ac32 (ExpressionTool)
gather_dkfz_embl_snvs
preprocess_vcf.cwl#gather_dkfz_embl_snvs/4ef85793-84bd-42b0-a08f-63bbb793a2e6 (ExpressionTool)
populate_output_record
preprocess_vcf.cwl#populate_output_record/b0e62186-127e-4557-b8e3-7d8b4c15b5f2 (ExpressionTool)
gather_dkfz_embl_indels
preprocess_vcf.cwl#gather_dkfz_embl_indels/8c7b91e9-742f-4e72-8f51-a339476b5d23 (ExpressionTool)
null_filter_extracted_snvs
preprocess_vcf.cwl#null_filter_extracted_snvs/85193684-5784-438f-b1ff-75fd3b289ed9 (ExpressionTool)
gather_muse_snvs_for_cleaning
preprocess_vcf.cwl#gather_muse_snvs_for_cleaning/87e277d3-3d11-4923-a583-f547fea40730 (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