CWL Workflow: pcawg_annotate_wf.cwl

Workflow: pcawg_annotate_wf.cwl

Fetched 2025-11-11 05:38:53 GMT

Verified with cwltool version 3.1.20230201224320

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/Outputs

Unknown workflow license, check source repository.

Inputs

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

Steps

ID	Runs	Doc
preprocess_vcfs	preprocess_vcf.cwl (Workflow)	This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.
run_annotator_snvs	annotator_sub_wf.cwl (Workflow)	This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!
zip_annotated_vcfs	zip_and_index_vcf.cwl (Workflow)	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.
get_normalized_vcfs	pcawg_annotate_wf.cwl#get_normalized_vcfs/71d6ed73-6c60-433f-9587-84040210b203 (ExpressionTool)
run_annotator_indels	annotator_sub_wf.cwl (Workflow)	This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!
gather_annotated_vcfs	pcawg_annotate_wf.cwl#gather_annotated_vcfs/08d47f67-fa0e-4528-a84a-5837d2681937 (ExpressionTool)

Outputs

ID	Type	Label	Doc
annotated_files	File[]
annotated_files_indicies	File[]