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fix missing output files in test.yaml #1570

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merged 3 commits into from
May 12, 2022
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@mirpedrol mirpedrol commented May 12, 2022

Closes #1564

When output files are inside a folder (e.g. index files from bowtie2/align module), os.walk() needs the parameter followlinks=True when creating the test.yml file to be able to retrieve all files.

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 12, 2022

Codecov Report

Merging #1570 (e9be065) into dev (8f5989d) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev    #1570   +/-   ##
=======================================
  Coverage   64.72%   64.72%           
=======================================
  Files          54       54           
  Lines        6246     6246           
=======================================
  Hits         4043     4043           
  Misses       2203     2203           
Impacted Files Coverage Δ
nf_core/modules/test_yml_builder.py 48.40% <100.00%> (ø)

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@mirpedrol mirpedrol marked this pull request as ready for review May 12, 2022 13:45
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@ewels ewels left a comment

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Specifically if using softlinks, right? Can't see the source that triggered the error, but LGTM! 👍🏻

@ewels ewels merged commit bfcd66f into nf-core:dev May 12, 2022
@mirpedrol mirpedrol deleted the missing_testfiles branch May 17, 2022 12:56
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2 participants