Workflow: preprocess_vcf.cwl
Fetched 2025-10-31 03:00:33 GMT
Verified with cwltool version 3.1.20221201130942
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File |
Reference file, used for normalized INDELs |
|
| vcfdir | Directory |
The directory where the files are |
|
| out_dir | String |
The name of the output directory |
|
| filesToPreprocess | String[] |
The files to process |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_for_indel |
preprocess_vcf.cwl#filter_for_indel/6af10f3d-8f34-4216-b215-930ef031a09c
(ExpressionTool)
|
||
| populate_output_record |
preprocess_vcf.cwl#populate_output_record/39b37147-1096-409f-afa4-8ffe53304ec5
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb/preprocess_vcf.cwl
