Workflow: pcawg_annotate_wf.cwl
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 `
- Selected
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- Default Values
- Nested Workflows
- Tools
- 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 | Label | Doc |
---|---|---|---|
preprocess_vcfs |
preprocess_vcf.cwl
(Workflow)
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This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
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run_annotator_snvs |
annotator_sub_wf.cwl
(Workflow)
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This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
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zip_annotated_vcfs |
zip_and_index_vcf.cwl
(Workflow)
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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. |
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get_normalized_vcfs |
pcawg_annotate_wf.cwl#get_normalized_vcfs/71d6ed73-6c60-433f-9587-84040210b203
(ExpressionTool)
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run_annotator_indels |
annotator_sub_wf.cwl
(Workflow)
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This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
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gather_annotated_vcfs |
pcawg_annotate_wf.cwl#gather_annotated_vcfs/08d47f67-fa0e-4528-a84a-5837d2681937
(ExpressionTool)
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Outputs
ID | Type | Label | Doc |
---|---|---|---|
annotated_files | File[] | ||
annotated_files_indicies | File[] |
Permalink:
https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/pcawg_annotate_wf.cwl