The CWL workflow to execute the OxoG filter only. 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 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-oxog-filter/blob/master/pcawg_oxog_wf.cwl
You can run this workflow with this command:
$ cwltool --debug --relax-path-checks --non-strict ./pcawg_oxog_wf.cwl ./my_input_file.json > out 2> err &