Update containers

[rsuchecki]

Biocontainers deliver great value. In addition to small size at the reasonable cost of not always having access to (admitedly incorrectly) expected standard versions of linux tools such as awk, sed etc.

Standard biocontainers are one tool per container. This is ideal for most of our use cases with some exceptions,in particular aligners outputting SAM rather than BAM.

Multi-package containers can be quickly built by submitting a PR to https://github.com/BioContainers/multi-package-containers
This generates mamba containers - tool names and versions hashed in the name.

Biocontainers server(s) available with 40k singularity image files available

• https://cyverse-container-camp-workshop-2018.readthedocs-hosted.com/en/latest/biocontainer/biocontainers_hpc.html
• https://depot.galaxyproject.org/singularity/
• https://galaxyproject.github.io/training-material/topics/admin/tutorials/cvmfs/tutorial.html

[rsuchecki]

It appears that docker hub is no longer viable in terms of preserving containers long-term

https://twitter.com/nf_core/status/1294009631530917888

We already mostly use biocontainers but the overall setup needs to be overhauled.

Consider:

• quay.io for own/customised images
• GHA builds?
• Pivot to safely deposited simg?
  • https://depot.galaxyproject.org/singularity/
  • zenodo, other?
  • https://github.com/singularityhub/singularity2docker
• Re-consider conda as starting points -> biocontainers