Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2023-01-11 22:27:36 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 |
|---|---|---|---|
| vcfdir | Directory | ||
| out_dir | String | ||
| refFile | File | ||
| tumours | https://w3id.org/cwl/view/git/a7d65918c444ee3c99c56bd0f08c2ce670a853ed/TumourType.yaml#TumourType[] | ||
| normalBam | File | ||
| refDataDir | Directory | ||
| sv-padding | String | ||
| minibamName | String | ||
| snv-padding | String | ||
| indel-padding | String | ||
| inputFileDirectory | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gather_minibams |
oxog_varbam_annotate_wf.cwl#gather_minibams/84effc62-56d9-4a68-b5d5-36edf4252b48
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/e480f9ce-fd19-4024-b879-6ed4d985f996
(ExpressionTool)
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| 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)
|
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/df971d69-e27d-4148-83ef-94217c838533
(ExpressionTool)
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| get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/93d3e81f-3cb3-448c-9b9f-e8f6741e5497
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/ccec980d-c100-453b-8e52-928e67f5ca91
(ExpressionTool)
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| get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/9efd46f6-2670-40c9-94c7-f31bee6fb3b6
(ExpressionTool)
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| filter_merged_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/41e84bbb-1bdb-4fa0-b3c9-c96aa51fd2d4
(ExpressionTool)
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| get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/0e658d79-514b-4ae7-ab39-4aac587b03b8
(ExpressionTool)
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| gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/1fd4eb9e-c0d0-470d-89bc-d389bb6afc4a
(ExpressionTool)
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| run_annotator_indels |
annotator_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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| 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 |
|---|---|---|---|
| minibams | File[] |
Permalink:
https://w3id.org/cwl/view/git/a7d65918c444ee3c99c56bd0f08c2ce670a853ed/oxog_varbam_annotate_wf.cwl
