Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2023-01-08 23:25:03 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/b38a8a4785746b8267913ea5389e21ae6dc921a3/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/bf4f1871-9ef1-4bfa-ba51-a2c4d729a5be
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/04830d3f-f433-4c2d-9e6c-765062b2c600
(ExpressionTool)
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| preprocess_vcfs |
preprocess_vcf.cwl
(Workflow)
|
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! |
|
| filter_merged_sv |
oxog_varbam_annotate_wf.cwl#filter_merged_sv/6504e66d-5b8d-4bf7-a779-31f2c2d5b128
(ExpressionTool)
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| get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/99083dae-e635-40c3-8c8b-32a46acf8cf7
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/98561489-51d0-441e-85c2-eba4fcade696
(ExpressionTool)
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| get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/c5671b16-5406-4d90-a8fa-49887752c97d
(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/a1d50fc1-ef7e-4f15-842e-c02082fd219e
(ExpressionTool)
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| flatten_oxog_output |
oxog_varbam_annotate_wf.cwl#flatten_oxog_output/22a529fc-3651-4328-94ac-e274fa594c25
(ExpressionTool)
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| get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/14bec7f6-50c5-41b0-9240-e0f5439f0b89
(ExpressionTool)
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| gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/3158ba7f-62f8-4c14-be30-0e908d44f17d
(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/fbf8edb7-a55d-4e02-9e46-ad5b3352049b
(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/b38a8a4785746b8267913ea5389e21ae6dc921a3/oxog_varbam_annotate_wf.cwl
