Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2023-01-11 22:27:25 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/c162a19d83f872fe0dc0077e18bef22c99423e4d/TumourType.yaml#TumourType[] | ||
| normalBam | File | ||
| sv-padding | String | ||
| snv-padding | String | ||
| indel-padding | String | ||
| inputFileDirectory | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gather_minibams |
oxog_varbam_annotate_wf.cwl#gather_minibams/3fe68e68-6f5e-433b-9c4f-38c3e727d014
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/df09a001-55a7-4224-8dfd-024a91992e68
(ExpressionTool)
|
||
| preprocess_vcfs |
preprocess_vcf.cwl
(Workflow)
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This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
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| run_variant_bam |
minibam_sub_wf.cwl
(Workflow)
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This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow! |
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| filter_merged_sv |
oxog_varbam_annotate_wf.cwl#filter_merged_sv/6651636a-914e-40ea-9209-abaf65c33a5e
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/4896cafd-b9f7-4cfb-9c13-7234c181141e
(ExpressionTool)
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| filter_merged_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/1308459e-04d0-4db6-9416-59f95980879c
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| minibams | File[] |
Permalink:
https://w3id.org/cwl/view/git/c162a19d83f872fe0dc0077e18bef22c99423e4d/oxog_varbam_annotate_wf.cwl
