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diann 1.8.1 -> 1.9.1dev #381

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diann 1.8.1 -> 1.9.1dev #381

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ypriverol
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 96d1d1c

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-02 11:13:05

@ypriverol ypriverol mentioned this pull request Jul 2, 2024
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@vdemichev
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I am discontinuing the 'regular .speclib'. What will remain: .predicted.speclib for predicted libraries, and .skyline.speclib instead of regular .speclib. The thing here is that .speclib is in general quite non-transparent, i.e. the user cannot easily check what's in there, hence not the best for reproducibility. So DIA-NN now encourages users with warnings to only use either the .predicted.speclib or the .tsv library. The .skyline.speclib is there purely to be loaded automatically by Skyline, i.e. while it works fine as DIA-NN input in practice this will not be 'supported' - compatiblity might be incomplete in the future.

So in this case, can either use .skyline.speclib or (better) the .tsv library.

Now, about the empirical DIA-based .tsv lib. This will get replaced with .parquet, maybe even in the 1.9.1 update.

@ypriverol
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We are closing this PR. In the current LICENSE of DIANN, cloud infrastructures are not allowed.

@ypriverol ypriverol closed this Jul 4, 2024
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@ypriverol @vdemichev