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pcawg-minibam

The CWL workflow to generate minbiams 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

This CWL workflow uses Variantbam to generate minibams. for more information on Variantbam, see: https://github.com/walaj/VariantBam/

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-minibam/blob/develop/pcawg_minibam_wf.cwl

You can run this workflow with this command:

$ cwltool --debug --relax-path-checks --non-strict ./pcawg_minibam_wf.cwl ./my_input_file.json > out 2> err &