CWL Workflow: oxog_varbam_annotate_wf.cwl

Workflow: oxog_varbam_annotate_wf.cwl

Fetched 2023-01-11 23:03:53 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/9b7fde6e34f632ceb1d0e2b1a5799a6f722688c5/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/4ce43f14-61b0-4b14-a5d8-2652c14eecac (ExpressionTool)
get_merged_vcfs	oxog_varbam_annotate_wf.cwl#get_merged_vcfs/40d76022-c4dd-4988-bcc3-bee28b55bb32 (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/502e9950-7621-4858-9f73-6214d1bd3613 (ExpressionTool)
filter_merged_snv	oxog_varbam_annotate_wf.cwl#filter_merged_snv/795cabee-11ea-4a6d-bbef-7ec1685c91ea (ExpressionTool)
filter_merged_indel	oxog_varbam_annotate_wf.cwl#filter_merged_indel/49fcac35-5d52-465c-879c-822c0ed8360b (ExpressionTool)

Outputs

ID	Type	Label	Doc
minibams	File[]