Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2023-01-11 21:40:08 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/ad42ab7a8c7e190d5f8615b52278346262256424/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/6f8fd9f4-d142-4dcb-a03c-584c0eb85376
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/a4e6e96d-aa38-43ac-be8a-b6e90d9612b7
(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/316c9dba-ad3a-4f3e-b9bc-afc7e1c18b29
(ExpressionTool)
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| get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/c9cf32cf-f86b-4db5-ba4e-e372e565c050
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/15e9bd8a-5960-4bf7-b532-0cae701370b9
(ExpressionTool)
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| get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/6d44eb99-5e83-4159-9cfd-315541eab7dd
(ExpressionTool)
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| filter_merged_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/5bb6f271-8275-4a8f-ac96-d60f7ae8c8ff
(ExpressionTool)
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| get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/4e4aa6a9-8c0e-4ea7-83fe-2382e2d8ad7d
(ExpressionTool)
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| gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/b3c0e965-3595-41ae-80ee-3dd347d16e51
(ExpressionTool)
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| zip_and_index_files_for_oxog |
zip_and_index_vcf.cwl
(Workflow)
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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/ad42ab7a8c7e190d5f8615b52278346262256424/oxog_varbam_annotate_wf.cwl
