CWL Workflow: oxog_varbam_annotate_wf.cwl

Workflow: oxog_varbam_annotate_wf.cwl

Fetched 2023-01-11 21:37:21 GMT

Verified with cwltool version 3.1.20221201130942

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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Default Values
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Inputs/Outputs

Unknown workflow license, check source repository.

Inputs

ID	Type	Title	Doc
vcfdir	Directory
out_dir	String
refFile	File
tumours	https://w3id.org/cwl/view/git/f736cf8f663fbba8f1b4158431f2b6a6d88491b4/TumourType.yaml#TumourType[]
normalBam	File
refDataDir	Directory
sv-padding	String
minibamName	String
snv-padding	String
indel-padding	String
inputFileDirectory	Directory

Steps

ID	Runs	Doc
gather_minibams	oxog_varbam_annotate_wf.cwl#gather_minibams/b410d6ff-5b5d-425d-a3b0-e4c23895ecf9 (ExpressionTool)
get_merged_vcfs	oxog_varbam_annotate_wf.cwl#get_merged_vcfs/256c9187-2888-4948-b6cc-c9c431bff50d (ExpressionTool)
preprocess_vcfs	preprocess_vcf.cwl (Workflow)	This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.
run_variant_bam	minibam_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!
filter_merged_sv	oxog_varbam_annotate_wf.cwl#filter_merged_sv/d63c31ce-7325-450a-b8f6-281ad2585e23 (ExpressionTool)
filter_merged_snv	oxog_varbam_annotate_wf.cwl#filter_merged_snv/c3aa8477-33a9-4778-ad0d-78c1e67c2473 (ExpressionTool)
get_extracted_snvs	oxog_varbam_annotate_wf.cwl#get_extracted_snvs/3beda68a-4480-40d6-be51-e41eecc47b7b (ExpressionTool)
filter_merged_indel	oxog_varbam_annotate_wf.cwl#filter_merged_indel/04e77582-a94e-4ef1-8b60-fc0e9b512442 (ExpressionTool)
get_normalized_vcfs	oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/0f787f57-7eab-4e9b-88fe-1f8168523869 (ExpressionTool)

Outputs

ID	Type	Label	Doc
minibams	File[]