Hi,
For PCAWG workflows, we’re currently aware of the following workflows that have been successfully tested and published to Dockstore.
- BWA-mem https://dockstore.org/containers/quay.io/pancancer/pcawg-bwa-mem-workflow
- Sanger Variant call https://dockstore.org/containers/quay.io/pancancer/pcawg-sanger-cgp-workflow
- DKFZ Variant call https://dockstore.org/containers/quay.io/pancancer/pcawg-dkfz-workflow
- DELLY SV call https://dockstore.org/containers/quay.io/pancancer/pcawg_delly_workflow
- DKFZ Bias Filtering https://dockstore.org/containers/quay.io/jwerner_dkfz/DKFZBiasFilter
- SV Merge https://dockstore.org/containers/registry.hub.docker.com/weischenfeldt/pcawg_sv_merge
- SNV Consensus https://dockstore.org/containers/quay.io/pancancer/pcawg-consensus-caller
OxoG (variantBAM+OxoG), SNV Merge Annotate, Broad Variant call, the the PoN Index/SNV Filter are in progress.