Workflow: pcawg_minibam_wf.cwl
Fetched 2024-05-02 15:21:53 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
- |
- 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/e9f3694e31e3c1570183a4f444a44015766f9f2f/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/956aea88-4d2b-429f-b4cd-ca55345440ff
(ExpressionTool)
|
||
| get_merged_vcfs |
pcawg_minibam_wf.cwl#get_merged_vcfs/da724b92-9773-4094-a88f-aca7e985302e
(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/f116d4c3-4b2a-4365-b8e6-0ddde5c659ce
(ExpressionTool)
|
||
| filter_merged_snv |
pcawg_minibam_wf.cwl#filter_merged_snv/60fb032a-4bb5-46a9-9ca9-309d6680315c
(ExpressionTool)
|
||
| filter_merged_indel |
pcawg_minibam_wf.cwl#filter_merged_indel/551ca935-b481-4d10-99b7-cdaf23b27837
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| minibams | File[] |
Permalink:
https://w3id.org/cwl/view/git/e9f3694e31e3c1570183a4f444a44015766f9f2f/pcawg_minibam_wf.cwl
