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@awgymer awgymer commented Nov 22, 2022

Fixes #2041

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

@awgymer awgymer marked this pull request as ready for review November 22, 2022 13:24
@awgymer awgymer requested a review from mashehu November 22, 2022 13:24
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codecov bot commented Nov 22, 2022

Codecov Report

Merging #2042 (aefa3d5) into dev (bbb5415) will decrease coverage by 0.01%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##              dev    #2042      +/-   ##
==========================================
- Coverage   67.60%   67.58%   -0.02%     
==========================================
  Files          43       43              
  Lines        5572     5572              
==========================================
- Hits         3767     3766       -1     
- Misses       1805     1806       +1     
Impacted Files Coverage Δ
nf_core/__main__.py 58.45% <0.00%> (ø)
nf_core/components/remove.py 86.76% <100.00%> (ø)
nf_core/modules/lint/__init__.py 82.88% <0.00%> (-0.54%) ⬇️

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@mashehu
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mashehu commented Nov 22, 2022

Trying to add a test for this now. But it is somehow not working. 🤔

@awgymer
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awgymer commented Nov 22, 2022

Trying to add a test for this now. But it is somehow not working. 🤔

Which bit is failing? For now it will still only work with nf-core mirrors that also have nf-core as the "org" in the git path. The code to make it work with other repos is in my other branch.

@mashehu mashehu mentioned this pull request Nov 25, 2022
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awgymer commented Nov 25, 2022

Weird error in the CI:

Command error:
  Skipping 'SAMPLE3_SE_T2.fastq.gz' which didn't exist, or couldn't be read

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mashehu commented Nov 25, 2022

Weird error in the CI:

Just a hick-up with the test data repo, rerunning the test fixed it (known issue 😞)

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3 participants