Workflow: preprocessor_for_oxog.cwl
Fetched 2024-05-02 04:29:03 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 |
preprocessor_for_oxog.cwl#filter_for_indel/26497ccb-192c-4214-b454-5d48163ae203
(ExpressionTool)
|
||
| gather_clean_vcfs |
preprocessor_for_oxog.cwl#gather_clean_vcfs/1f2a41e4-216a-4496-87cf-f4a769c94e3f
(ExpressionTool)
|
||
| populate_output_record |
preprocessor_for_oxog.cwl#populate_output_record/033cc8e8-0cba-467f-815b-d88a20d551bd
(ExpressionTool)
|
||
| null_filter_extracted_snvs |
preprocessor_for_oxog.cwl#null_filter_extracted_snvs/4852dfab-eb4a-47aa-8f61-792293fdb64d
(ExpressionTool)
|
||
| gather_muse_snvs_for_cleaning |
preprocessor_for_oxog.cwl#gather_muse_snvs_for_cleaning/88f7ca41-ea8e-426f-a4d4-1d75d2eb6deb
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| preprocessedFiles | https://w3id.org/cwl/view/git/cf1f7f985c72cdf6ee0db386791c921376265486/PreprocessedFilesType.yaml#PreprocessedFileset |
Permalink:
https://w3id.org/cwl/view/git/cf1f7f985c72cdf6ee0db386791c921376265486/preprocessor_for_oxog.cwl
