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Add fail-warned to pipeline linting workflow #1593

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merged 10 commits into from
May 31, 2022

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@mirpedrol mirpedrol commented May 18, 2022

The GitHub workflow for pipeline linting does not fail on warnings.

  • Add --fail-warned option to nf-core lint to make the warnings fail.
  • Remove TODO statements from template pipeline in the linting workflow. Those lines are expected to produce a warning during linting.
  • Add --fail-warned to pipeline linting workflow

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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codecov bot commented May 18, 2022

Codecov Report

Merging #1593 (dd6d0a1) into dev (34d472f) will increase coverage by 0.08%.
The diff coverage is 81.81%.

@@            Coverage Diff             @@
##              dev    #1593      +/-   ##
==========================================
+ Coverage   64.63%   64.71%   +0.08%     
==========================================
  Files          54       54              
  Lines        6249     6235      -14     
==========================================
- Hits         4039     4035       -4     
+ Misses       2210     2200      -10     
Impacted Files Coverage Δ
nf_core/__main__.py 50.66% <66.66%> (+0.11%) ⬆️
nf_core/lint/__init__.py 74.59% <87.50%> (+1.20%) ⬆️
nf_core/lint/files_unchanged.py 73.33% <0.00%> (-2.67%) ⬇️
nf_core/lint_utils.py 86.66% <0.00%> (-0.44%) ⬇️
nf_core/modules/bump_versions.py 64.60% <0.00%> (-0.23%) ⬇️
nf_core/sync.py 52.23% <0.00%> (-0.22%) ⬇️
nf_core/modules/lint/__init__.py 82.52% <0.00%> (-0.19%) ⬇️
nf_core/list.py 79.91% <0.00%> (ø)
nf_core/create.py 85.93% <0.00%> (ø)
nf_core/schema.py 77.24% <0.00%> (ø)
... and 36 more

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@mirpedrol mirpedrol marked this pull request as ready for review May 19, 2022 08:44
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@ggabernet ggabernet left a comment

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Looks good to me!

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Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
@mirpedrol mirpedrol merged commit dc4e8f1 into nf-core:dev May 31, 2022
@mirpedrol mirpedrol deleted the fail_warned branch June 2, 2022 13:33
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2 participants