Maxime U Garcia

DO NOT MERGE yet as it'll break `tools` if you don't have the current `dev` (modules updates)

Nothing yet in Bioconda. What would be your use case with somalier?

Hi @mvelinder both are tools that we indeed considered. At the time of #105 deepvariant seemed to big to be integrated into sarek. with DSL2, it would make sense to...

Currently not providing a download script for cache and other files for annotation

Hi @grendon First congratulations, we don't have many people running Sentieon with sarek. I'm always happy to see other people do it. Unfortunately, the small number of people using this...

> * straightforward output for multiqc (tsv tables are produced automatically --> could just report this in separate table in MultiQC report in Sarek) heavy_check_mark MultiQC module possibility even?

I'd say we go for CRAM everywhere.

Should be easy enough to cover both, no?

Needs more data than that for Sarek (cf: https://github.com/nf-core/sarek/blob/05194ed421d7fef6b7cef05fe267a95d8ceb4d6c/conf/igenomes.config#L36-L57)

that's the flag when running the pipeline. I haven't find a similar flag in the help for tools. The one close is `-r` `--revision` but it targets a pipeline, not...