Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2024-04-26 12:16:17 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
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vcfdir | Directory | ||
| out_dir | String | ||
| refFile | File | ||
| tumours | https://w3id.org/cwl/view/git/40bf56daf9edab82e0f964dbd6961ca1111cd35f/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 |
|---|---|---|---|
| qa_check | |||
| run_oxog |
oxog_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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| gather_minibams |
oxog_varbam_annotate_wf.cwl#gather_minibams/57b270d5-b9d7-4a62-a7de-6d2d7053c427
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/6529e75d-b7c0-4ea3-8a18-de54eeb6ba30
(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/aea0e66c-004b-45c2-83f9-31ce995ba5ab
(ExpressionTool)
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| get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/f0b27dda-5f83-488a-a09d-a83d4cef3b43
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/df86b06e-4e1b-4e23-ab82-2ecab252929e
(ExpressionTool)
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| get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/50d0761b-42ca-4915-8eb0-15461386556d
(ExpressionTool)
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| run_annotator_snvs |
annotator_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_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/e8a9f986-3ea8-46ab-ad89-88f8e1c006dd
(ExpressionTool)
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| flatten_oxog_output |
oxog_varbam_annotate_wf.cwl#flatten_oxog_output/fb3c1d3f-d874-4943-aca5-0993d71db2d3
(ExpressionTool)
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| get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/71623b97-913e-4109-b470-a969464a792e
(ExpressionTool)
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| gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/343c877f-533f-4bc2-8793-1304d77774e8
(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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| gather_annotated_vcfs |
oxog_varbam_annotate_wf.cwl#gather_annotated_vcfs/c171f615-39a8-4ac1-bc6c-29f65b13a09f
(ExpressionTool)
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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[] | ||
| annotated_files | File[] | ||
| oxog_filtered_files | File[] |
https://w3id.org/cwl/view/git/40bf56daf9edab82e0f964dbd6961ca1111cd35f/oxog_varbam_annotate_wf.cwl
