Workflow: pcawg_oxog_wf.cwl
Fetched 2024-04-18 04:34:18 GMT
Verified with cwltool version 3.1.20221201130942
This workflow will perform OxoG filtering on a set of VCFs. It will produce VCFs and their associated index files.
- Selected
- |
- 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/cf1f7f985c72cdf6ee0db386791c921376265486/TumourType.yaml#TumourType[] | ||
| refDataDir | Directory | ||
| inputFileDirectory | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_oxog |
oxog_sub_wf.cwl
(Workflow)
|
This is a subworkflow - this is not meant to be run as a stand-alone workflow! |
|
| get_cleaned_vcfs |
pcawg_oxog_wf.cwl#get_cleaned_vcfs/7ea7046e-ee27-4561-93a7-348f9fa2e9f6
(ExpressionTool)
|
||
| preprocess_files |
preprocessor_for_oxog.cwl
(Workflow)
|
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
|
| get_extracted_snvs |
pcawg_oxog_wf.cwl#get_extracted_snvs/836923d1-7df8-40eb-be73-4ce2e2462c33
(ExpressionTool)
|
||
| flatten_oxog_output |
pcawg_oxog_wf.cwl#flatten_oxog_output/9a539dd9-dbf3-4f04-a5a7-26a8dc5cd8bc
(ExpressionTool)
|
||
| gather_vcfs_for_oxog |
pcawg_oxog_wf.cwl#gather_vcfs_for_oxog/456ad246-9832-48d1-bb17-f446007e264f
(ExpressionTool)
|
||
| flatten_oxog_tbi_output |
pcawg_oxog_wf.cwl#flatten_oxog_tbi_output/78c28202-a1e6-4cfe-8806-95b6e6773cfc
(ExpressionTool)
|
||
| zip_and_index_files_for_oxog |
zip_and_index_vcf.cwl
(Workflow)
|
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. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| oxogTBIs | File[] | ||
| oxogVCFs | File[] |
Permalink:
https://w3id.org/cwl/view/git/cf1f7f985c72cdf6ee0db386791c921376265486/pcawg_oxog_wf.cwl
