2311 interpret docker.registry automatically

[adamrtalbot]

Based on #2313 which is based on #2306 so this is likely to get messy.

• feat (2311): Infer docker.registry value from nextflow.config
• Update test

Fixes #2310

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 #2318 (10f1807) into dev (887e83e) will increase coverage by 0.00%.
The diff coverage is 90.00%.

@@           Coverage Diff           @@
##              dev    #2318   +/-   ##
=======================================
  Coverage   72.90%   72.90%           
=======================================
  Files          78       78           
  Lines        8761     8767    +6     
=======================================
+ Hits         6387     6392    +5     
- Misses       2374     2375    +1     

Impacted Files	Coverage Δ
nf_core/__main__.py	57.16% <ø> (ø)
nf_core/modules/lint/__init__.py	83.41% <87.50%> (-0.01%)	⬇️
nf_core/utils.py	81.40% <100.00%> (ø)

[mirpedrol]

LGTM, only one small comment

[mirpedrol]

is this function used?

[adamrtalbot]

No I don't think it is!

[adamrtalbot]

@mirpedrol There is a slight problem where it only looks for the most basic nextflow.config file. You can override the registry on the command line but do we want it to be more intelligent?

[mirpedrol]

This is only for linting modules, right? If I'm not wrong, we will always provide the registry through a nextflow.config file in nf-core/modules. In that case, I think it's fine that it only checks nextflow.config. Or is there any edge case that I am missing?

[adamrtalbot]

It is also used with pipelines I believe, so people may override the standard registry with that. As long as it's in the /nextflow.config (pipeline) or tests/config/nextflow.config (modules) it should work.

[adamrtalbot]

Oh but fetch_wf_config() runs nextflow config -flat. So maybe it's OK?

[mirpedrol]

Not sure I'm following, do you mean that fetch_wf_config() does only retrieve configuration values from nextflow.config?

[mirpedrol]

Ok I think I misunderstood your first question, sorry!

Oh but fetch_wf_config() runs nextflow config -flat. So maybe it's OK?

Now I have double-checked this and I think it's ok :) nextflow config will return all the configuration values