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Related Issues (20)
- New Sniffles2 (sub)workflow HOT 1
- Update all docker images to have as few layers as possible.
- Review tasks / scripts in docker containers and remove redundant functionality
- Review docker images for mixing of `pip` and `conda` environments
- Review repo / code organization; write development guide. HOT 1
- Review docker base images for non-LTS versions of Ubuntu (and other OSes)
- Pin versions for every dependency in docker / venv / conda environments.
- Complete implementation of `lr-ref`
- Review `lr-utils` conda / python envs. HOT 1
- Next iteration of WDL validator should enforce documentation HOT 1
- Consider saving WGS FASTQ outputs in CoLoRd format
- Go through the outputs of miniwdl check to clean up
- Replace LRConvertBCF workflow with a more efficient and up-to-date solution
- CNV pipeline needs to finalize results
- Investigate if finalization steps could be improved with `gcloud storage cp`
- ONTProcessBasecall Input Issue
- update all pacbio software to those packaged in the SMRTLink release
- Make Finalize.wdl tasks volatile
- Long read pipeline Canu issue with Mouse Genome reference HOT 2
- Migrate all viable docker images to google artifact registry
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