Workflow: oxog_varbam_annotate_wf.cwl
Fetched 2024-11-25 08:02:26 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/6366ed398da10019b6d81a789291af6d909f28f4/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/9fb2663a-6fa1-4407-92d5-62ad6f64a62c
(ExpressionTool)
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| get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/94c72726-f499-4c7f-a16d-b84cce179edf
(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! |
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| filter_merged_sv |
oxog_varbam_annotate_wf.cwl#filter_merged_sv/8f1cb245-62cf-44d0-9642-5c4c54257adb
(ExpressionTool)
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| get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/b9cf5b1d-e364-4ed9-ac24-5e217b7c7130
(ExpressionTool)
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| filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/59c7ac98-585b-4b9f-aadd-2d7057d7c17c
(ExpressionTool)
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| get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/919652cf-a2d7-4d4a-b721-319e26d5656e
(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/2eb5e7bc-5724-4b08-8c63-454f41bce2b0
(ExpressionTool)
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| flatten_oxog_output |
oxog_varbam_annotate_wf.cwl#flatten_oxog_output/532b225b-c006-407d-8d59-27b5d3079eb3
(ExpressionTool)
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| get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/af128324-8a20-41b5-9f55-82080e0b57bc
(ExpressionTool)
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| gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/16b94a43-4958-4abd-bfd7-7c286de589be
(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/85b14890-5e48-45f0-81d9-1bb450d91c70
(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/6366ed398da10019b6d81a789291af6d909f28f4/oxog_varbam_annotate_wf.cwl
