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Explicitly disable conda container profiles #2140

Merged
merged 3 commits into from
Dec 23, 2022
Merged

Explicitly disable conda container profiles #2140

merged 3 commits into from
Dec 23, 2022

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jfy133
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@jfy133 jfy133 commented Dec 23, 2022 •
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This ensures consistency across all profiles that only one software environment system is selected at any one time.

This also allows complete 'evaluation' of what container system is being used within a given pipeline run.

This was motivated by: https://github.com/nf-core/modules/pull/2688/files where we have to check if conda is enabled with session.config.conda.enabled.

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

@jfy133 jfy133 changed the base branch from master to dev December 23, 2022 09:34
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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

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/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 nf-core/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!

jfy133
jfy133 commented Dec 23, 2022
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nvnieuwk
nvnieuwk approved these changes Dec 23, 2022
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LGTM, happy holidays! 🎄

JoseEspinosa
JoseEspinosa approved these changes Dec 23, 2022
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LGTM

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codecov bot commented Dec 23, 2022

Codecov Report

Merging #2140 (a09c060) into dev (39c6bcd) will decrease coverage by 0.02%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev    #2140      +/-   ##
==========================================
- Coverage   71.43%   71.41%   -0.03%     
==========================================
  Files          77       77              
  Lines        8367     8367              
==========================================
- Hits         5977     5975       -2     
- Misses       2390     2392       +2
Impacted Files Coverage Δ
nf_core/modules/test_yml_builder.py 51.11% <0.00%> (-0.89%) ⬇️

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@ewels ewels merged commit 69060a8 into dev Dec 23, 2022
@ewels ewels deleted the explicitly-disable-conda-container-profiles branch December 23, 2022 09:48
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@ewels ewels ewels approved these changes

@mashehu mashehu Awaiting requested review from mashehu

@mirpedrol mirpedrol Awaiting requested review from mirpedrol

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4 participants
@jfy133 @ewels @JoseEspinosa @nvnieuwk