Modules Docker containers no longer includes quay.io as prefix

[adamrtalbot]

All modules will by default use relative Docker URI now, e.g. biocontainers/fastqc instead of quay.io/biocontainers/fastqc. Instead, quay.io should be set at the pipeline level (see #2233). The module creation should work as before and singularity is untouched.

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

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @adamrtalbot,

It looks like this pull-request is has been made against the adamrtalbot/tools master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the adamrtalbot/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[mirpedrol]

I think we will also have to modify the function get_biocontainer_tag which gets the container link so it doesn't include "quai.io" in the output.

[codecov]

Codecov Report

Merging #2249 (fc95246) into dev (271b84c) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev    #2249   +/-   ##
=======================================
  Coverage   73.19%   73.20%           
=======================================
  Files          77       77           
  Lines        8429     8432    +3     
=======================================
+ Hits         6170     6173    +3     
  Misses       2259     2259           

Impacted Files	Coverage Δ
nf_core/download.py	52.72% <ø> (ø)
nf_core/modules/bump_versions.py	63.90% <ø> (ø)
nf_core/modules/lint/main_nf.py	68.09% <100.00%> (+0.21%)	⬆️
nf_core/utils.py	82.41% <100.00%> (+0.03%)	⬆️

[mirpedrol]

I made this change to remove "quay.io" from the url when we obtain it automatically through the API. Sounds good?

[adamrtalbot]

I made this change to remove "quay.io" from the url when we obtain it automatically through the API. Sounds good?

That looks good. Can we manually include quay.io still? Most modules will still be quay.io/biocontainers/tool for a while.

Leaving quay.io at the front doesn't cause any issues, it's just explicit. This will help us with the migration once I try and make these changes in nf-core/modules.

[mirpedrol]

This is affecting the creation of new modules, so won't affect the current ones. We do want to create all new modules without quay.io, right? Or do we have to wait until the migration?

[adamrtalbot]

This is affecting the creation of new modules, so won't affect the current ones. We do want to create all new modules without quay.io, right? Or do we have to wait until the migration?

By default, don't include quay.io but a module developer can add it back in if necessary. E.g., mulled containers are only on quay.io so we will need to specify the entire URI quay.io/biocontainers/mulled-....

[mirpedrol]

ok, got it 👍 In that case developers can add it manually :)