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Lint for container names #1683

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merged 5 commits into from
Jul 21, 2022

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ErikDanielsson
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@ErikDanielsson ErikDanielsson commented Jul 19, 2022

Added lint test to check that the container names in modules are parsable, as was suggested in #1654. To have the possibility of making the warned module lint test more prominent, I also added a --fail-warned flag. This flag is not activated when nf-core lint is run with its --fail-warned flag, since this will make the "Create and lint pipeline" GH action fail. (An idea on how to solve this is suggested in #1684)

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

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@ErikDanielsson ErikDanielsson changed the base branch from master to dev July 19, 2022 14:10
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codecov bot commented Jul 19, 2022

Codecov Report

Merging #1683 (c291c8d) into dev (dc667c9) will increase coverage by 0.14%.
The diff coverage is 75.00%.

@@            Coverage Diff             @@
##              dev    #1683      +/-   ##
==========================================
+ Coverage   67.99%   68.13%   +0.14%     
==========================================
  Files          56       56              
  Lines        6614     6637      +23     
==========================================
+ Hits         4497     4522      +25     
+ Misses       2117     2115       -2     
Impacted Files Coverage Δ
nf_core/download.py 54.08% <0.00%> (ø)
nf_core/modules/lint/main_nf.py 66.53% <70.58%> (+1.16%) ⬆️
nf_core/modules/lint/__init__.py 84.79% <81.81%> (+1.93%) ⬆️
nf_core/__main__.py 52.46% <100.00%> (+0.10%) ⬆️
nf_core/utils.py 80.56% <100.00%> (+0.03%) ⬆️
nf_core/lint/__init__.py 74.07% <0.00%> (+0.41%) ⬆️

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Looks good! I think this will be really helpful :) thanks!

@ErikDanielsson ErikDanielsson merged commit d363205 into nf-core:dev Jul 21, 2022
@ErikDanielsson ErikDanielsson deleted the lint-singularity-image branch July 26, 2022 07:38
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Lint for singularity image parsing
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