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Centrifuge update to address mkfifo clashes #444

Merged
merged 6 commits into from
Feb 6, 2024
Merged

Centrifuge update to address mkfifo clashes #444

merged 6 commits into from
Feb 6, 2024

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jfy133
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@jfy133 jfy133 commented Feb 3, 2024

Hopefully 🤞 fixes #422

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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@jfy133 jfy133 changed the base branch from master to dev February 3, 2024 14:53
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github-actions bot commented Feb 3, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/taxprofiler master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/taxprofiler dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
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github-actions bot commented Feb 3, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit f9aee61

+| ✅ 195 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-05 16:03:54

jfy133
jfy133 commented Feb 3, 2024
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Super!!! Well done!!! I will test it now and will approve it once the job is completed.

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jfy133 commented Feb 5, 2024

I hope it works 🤞

LilyAnderssonLee
LilyAnderssonLee approved these changes Feb 5, 2024
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@LilyAnderssonLee LilyAnderssonLee left a comment •
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I don't have any issues regarding mkfifo, but instead, we don't get the correct *centrifuge.txt file. It seems that centrifuge-kreport didn't perform correctly. *.centrifuge.report.txt and *centrifuge.results.txt are correct.

Example of the file *centrifuge.txt

  0.52  42517   42517   U       0       unclassified
 99.48  8134168 8134168 -       1

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Update CHANGELOG.md
003bad1 
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
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jfy133 commented Feb 5, 2024

@sofstam I can't see your comment now, but yes I'm a bit concerned that the tests are failing :( need to investigate what that's meaning...

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sofstam commented Feb 5, 2024

@sofstam I can't see your comment now, but yes I'm a bit concerned that the tests are failing :( need to investigate what that's meaning...

I deleted it, I think Lili has an updated comment now.

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@jfy133 Have you tested the new version of Centrifuge-kreport in standalone mode?

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jfy133 commented Feb 5, 2024

No I didn't... my understanding from the release it wasn't meant to change...

https://github.com/DaehwanKimLab/centrifuge/releases/tag/v1.0.4.1

How does it look in your own test run/data?

@jfy133 jfy133 marked this pull request as draft February 5, 2024 10:33
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jfy133 commented Feb 5, 2024

OK found the problem, it was a bug in my bioconda recipe (bad docs)... going to go back and update the recipe and the biocontainer and the moduel... 😅

@jfy133 jfy133 marked this pull request as ready for review February 5, 2024 19:43
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jfy133 commented Feb 5, 2024

@LilyAnderssonLee final check?

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The test run for my real data was finished successfully this time. Got all correct files!!!
LGTM!

@jfy133 jfy133 merged commit 1e414ef into dev Feb 6, 2024
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@jfy133 jfy133 deleted the centrifuge-update branch February 6, 2024 08:53
@skrakau skrakau mentioned this pull request Feb 29, 2024
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

@Joon-Klaps Joon-Klaps Awaiting requested review from Joon-Klaps

@Midnighter Midnighter Awaiting requested review from Midnighter

@sofstam sofstam Awaiting requested review from sofstam

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Centrifuge error : (ERR): mkfifo(/tmp/72.inpipe1) failed.
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@jfy133 @LilyAnderssonLee @sofstam