https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation
This workflow performs annotation on SNV and INDEL VCFs.
https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation
cwl cwl-workflow indel-annotation pcawg snv-annotation
Last synced: over 1 year ago
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This workflow performs annotation on SNV and INDEL VCFs.
- Host: GitHub
- URL: https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation
- Owner: ICGC-TCGA-PanCancer
- Created: 2017-12-01T14:33:34.000Z (over 8 years ago)
- Default Branch: develop
- Last Pushed: 2018-02-05T20:22:05.000Z (over 8 years ago)
- Last Synced: 2023-08-13T02:16:19.814Z (almost 3 years ago)
- Topics: cwl, cwl-workflow, indel-annotation, pcawg, snv-annotation
- Language: JavaScript
- Homepage:
- Size: 127 KB
- Stars: 4
- Watchers: 5
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
Awesome Lists containing this project
README
# pcawg-snv-indel-annotation
This repository hosts the PCAWG Annotator as a CWL workflow. This workflow will _only_ run the annotator. For a workflow that runs PCAWG OxoG Filter, PCAWG Annotation, and generates Minibams, see this repository: https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools
The Anntoator was created by Jonathan Dursi. For more information, see this repo: https://github.com/ljdursi/sga-annotate-docker
The original SeqWare workflow can be found here: https://github.com/ICGC-TCGA-PanCancer/OxoGWrapperWorkflow
The Seqware workflow runs: the OxoG filter, produces mini-bams, and also runs Jonathan Dursi's PCAWG Annotator.
To visualize _this_ workflow, see here: https://view.commonwl.org/workflows/github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation/blob/develop/pcawg_annotate_wf.cwl
You can run this workflow with the following command:
```
$ cwltool --debug --relax-path-checks --non-strict ./pcawg_annotate_wf.cwl ./my_input_file.json > out 2> err &
```