Default Docker registry in template is quay.io

[adamrtalbot]

Sets the default container registry to quay.io. This can be modified directly using the config. For example, docker.registry = mysecret.registry.io and a process with container specified as multiqc:dev will result in mysecret.registry.io/multiqc:dev, however specifying the full URL such as quay.io/biocontainers/multiqc:latest will result in that container being used instead.

This shouldn't affect existing modules except in the case here someone is pulling an image from docker.io and has specified it using the container name only (e.g. ubuntu:20.04). This is likely to be pipeline specific and should be resolved pipeline side anyway.

Fixes #1948

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #2233 (f018d63) into dev (9e7f50e) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #2233   +/-   ##
=======================================
  Coverage   73.06%   73.06%           
=======================================
  Files          77       77           
  Lines        8404     8404           
=======================================
  Hits         6140     6140           
  Misses       2264     2264           

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[adamrtalbot]

This doesn't seem to work on cloud. Closing until we know more.

[adamrtalbot]

Turns out it should be fine on cloud, however when using Tower you must set the parameter directly in the config, e.g.:

docker.registry = "myregistry.io"

[adamrtalbot]

@mirpedrol what do you think of this? It's kinda dumb and I'm not 100% but it's the best idea I've had so far.

[mirpedrol]

Looks good, not sure if there are some weird cases where it will fail, but I think it will work for now

[mirpedrol]

Will need to merge this one for tests in #2249 to pass. Are you happy with merging? I was wondering if we should expose the parameter registry as you did in your POC?

[adamrtalbot]

I chatted with @drpatelh about this, we think if you're advanced enough to use a custom registry you should set it via config.

[adamrtalbot]

Will need to merge this one for tests in #2249 to pass. Are you happy with merging? I was wondering if we should expose the parameter registry as you did in your POC?

I'll rebase that branch now, but yes I think this one is good to go. We need to have a notice alerting pipeline developers to the change. Before we merge, is there anywhere good I can add this or shall we stick with documentation and Slack?

[mirpedrol]

Slack will be the best place to inform about the change 🙂

[adamrtalbot]

I've applied the template change to RNASeq to give it a thorough test, will merge if it works (looking good so far).