Workflow: pcawg_annotate_wf.cwl

Fetched 2018-12-15 07:56:55 GMT

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

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Inputs

ID Type Title Doc
oxogVCFs File[]
refFile File
inputFileDirectory Directory
out_dir String
tumourBams File[]
tumours https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/TumourType.yaml#TumourType[]
normalBam File

Steps

ID Runs Label Doc
zip_annotated_vcfs

This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output.

preprocess_vcfs
preprocess_vcf.cwl (Workflow)

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

gather_annotated_vcfs
pcawg_annotate_wf.cwl#gather_annotated_vcfs/ec108c72-a2a0-4cfa-90cf-a356ea54603b (ExpressionTool)
run_annotator_snvs

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

get_normalized_vcfs
pcawg_annotate_wf.cwl#get_normalized_vcfs/7ebb81d4-4f7b-486f-9148-cb875841fcda (ExpressionTool)
run_annotator_indels

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

Outputs

ID Type Label Doc
annotated_files_indicies File[]
annotated_files File[]
Permalink: https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/pcawg_annotate_wf.cwl