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Refgenie alias translation #2242

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merged 5 commits into from
Apr 25, 2023
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@mirpedrol mirpedrol commented Apr 20, 2023

Solves the problem reported on slack.

When the asset alias in a refgenie server is different to the one the nf-core pipeline expects, assets aren't detected. This allows having a translation files to automatically translate refgenie aliases to the ones used in nf-core.

Docs: nf-core/website#1754

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

@mirpedrol mirpedrol changed the base branch from master to dev April 20, 2023 13:51
@mirpedrol mirpedrol marked this pull request as ready for review April 24, 2023 09:15
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codecov bot commented Apr 24, 2023

Codecov Report

Merging #2242 (46a3c38) into dev (fa05c3c) will increase coverage by 0.02%.
The diff coverage is 85.00%.

@@            Coverage Diff             @@
##              dev    #2242      +/-   ##
==========================================
+ Coverage   73.04%   73.07%   +0.02%     
==========================================
  Files          77       77              
  Lines        8344     8364      +20     
==========================================
+ Hits         6095     6112      +17     
- Misses       2249     2252       +3     
Impacted Files Coverage Δ
nf_core/refgenie.py 77.41% <85.00%> (+2.07%) ⬆️

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nf_core/refgenie.py Show resolved Hide resolved
@mirpedrol mirpedrol added this to the 2.8 milestone Apr 25, 2023
@mirpedrol mirpedrol merged commit 6d52180 into nf-core:dev Apr 25, 2023
@mirpedrol mirpedrol deleted the refgenie-alias-translation branch April 25, 2023 11:50
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2 participants