Workflow: oxog_varbam_annotate_wf.cwl
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/96324c1392b6b774498e415346956e77e5d8dd86/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 |
---|---|---|---|
run_oxog |
oxog_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_minibams |
oxog_varbam_annotate_wf.cwl#gather_minibams/8b48b950-3438-4a0a-b539-df4425d756ed
(ExpressionTool)
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get_merged_vcfs |
oxog_varbam_annotate_wf.cwl#get_merged_vcfs/6e67730c-7efe-424b-a748-6c059e0dd0d8
(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)
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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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filter_merged_sv |
oxog_varbam_annotate_wf.cwl#filter_merged_sv/17a892bf-e5df-4e01-954b-1d66715bfb14
(ExpressionTool)
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get_cleaned_vcfs |
oxog_varbam_annotate_wf.cwl#get_cleaned_vcfs/3d21c588-452d-4824-943f-d18dbbb83eb8
(ExpressionTool)
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filter_merged_snv |
oxog_varbam_annotate_wf.cwl#filter_merged_snv/26a33ebb-bdcc-4aa7-b3f5-9003d1f68be6
(ExpressionTool)
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get_extracted_snvs |
oxog_varbam_annotate_wf.cwl#get_extracted_snvs/f9f95dfe-de6e-4757-b7fd-797bb7f196e2
(ExpressionTool)
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run_annotator_snvs |
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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filter_merged_indel |
oxog_varbam_annotate_wf.cwl#filter_merged_indel/a53e66ee-76b7-4693-b30e-357c06a2caa0
(ExpressionTool)
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flatten_oxog_output |
oxog_varbam_annotate_wf.cwl#flatten_oxog_output/b8b3906b-b647-4de3-89cd-ce7d52ccaac4
(ExpressionTool)
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get_normalized_vcfs |
oxog_varbam_annotate_wf.cwl#get_normalized_vcfs/db0752b3-fbda-4ab8-a7ac-5fba84b7f64b
(ExpressionTool)
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gather_vcfs_for_oxog |
oxog_varbam_annotate_wf.cwl#gather_vcfs_for_oxog/10a0a56d-ee0d-4c97-8ac3-ce2ad371e1ae
(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)
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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[] |
https://w3id.org/cwl/view/git/96324c1392b6b774498e415346956e77e5d8dd86/oxog_varbam_annotate_wf.cwl