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Tests changed, move them to test-datasets #167

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merged 31 commits into from
May 1, 2022
Merged

Tests changed, move them to test-datasets #167

merged 31 commits into from
May 1, 2022

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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 (nextflow run . -profile 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).

@ypriverol
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Please do not merge yet.

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github-actions bot commented Apr 29, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2626e22

+| ✅ 143 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-01 17:24:32

@ypriverol ypriverol mentioned this pull request Apr 29, 2022
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jpfeuffer
jpfeuffer reviewed Apr 29, 2022
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Nice. Can you refactor the contrast parsing logic as well?

@ypriverol
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@jpfeuffer I have reversed the changes because testing here in conda it works but for containers we may need to create a multi-tools container in biocontainers using the Msstats + here, should we go in that route or leave two scripts with repeated code?

jpfeuffer
jpfeuffer reviewed May 1, 2022
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jpfeuffer
jpfeuffer reviewed May 1, 2022
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@ypriverol @jpfeuffer
Update bin/msstats_plfq.R
60c8a36 
Co-authored-by: Julianus Pfeuffer <[email protected]>
@ypriverol @jpfeuffer
Update modules/local/msstats/main.nf
280dd6d 
Co-authored-by: Julianus Pfeuffer <[email protected]>
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Last thing, can you refactor msstats_tmt in the same way? E.g. put the functions on the top with a comment?

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ypriverol commented May 1, 2022 •
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Last thing, can you refactor msstats_tmt in the same way? E.g. put the functions on the top with a comment?

Last commit!!! 😉. I repeated even in the tmt, functions that are not needed, that comes from lfq for easy merge and refactoring in the future.

@ypriverol ypriverol added the enhancement New feature or request label May 1, 2022
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@jpfeuffer take a look

@jpfeuffer jpfeuffer merged commit 7aaf0e4 into bigbio:dev May 1, 2022
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