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 &