Workflow: pcawg_minibam_wf.cwl
Fetched 2023-01-04 02:50:31 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 `
- 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/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/TumourType.yaml#TumourType[] | ||
| normalBam | File | ||
| sv-padding | String | ||
| snv-padding | String | ||
| indel-padding | String | ||
| inputFileDirectory | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gather_minibams |
pcawg_minibam_wf.cwl#gather_minibams/b52e9e55-39aa-463f-ba07-8415048d9729
(ExpressionTool)
|
||
| get_merged_vcfs |
pcawg_minibam_wf.cwl#get_merged_vcfs/51f9e975-29f5-452a-9f53-589ced617c88
(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 |
pcawg_minibam_wf.cwl#filter_merged_sv/4f155948-3006-437d-9cec-5f978c9845e5
(ExpressionTool)
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||
| filter_merged_snv |
pcawg_minibam_wf.cwl#filter_merged_snv/fd3f3f7d-4883-44fc-80a1-c464bf9c2e07
(ExpressionTool)
|
||
| filter_merged_indel |
pcawg_minibam_wf.cwl#filter_merged_indel/49da7dc7-b732-4f07-98c2-e6c3b9103651
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| minibams | File[] |
Permalink:
https://w3id.org/cwl/view/git/e9f212b6e4c5b8ea691d9112c57201f498cf5dfe/pcawg_minibam_wf.cwl
