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Update bbduk memory parsing to prevent incompatibility with Java -xmx flag #635

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Merged
merged 2 commits into from
Aug 22, 2025
Merged

Update bbduk memory parsing to prevent incompatibility with Java -xmx flag #635

merged 2 commits into from
Aug 22, 2025

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jfy133
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@jfy133 jfy133 commented Aug 22, 2025

Thanks to @mahesh-panchal for the fix!

Close #632

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This PR is against the master branch ❌

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  • 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.

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Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev August 22, 2025 07:13
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github-actions bot commented Aug 22, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eaa4a65

+| ✅ 291 tests passed       |+
!| ❗  19 tests had warnings |!

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-22 07:17:05

erikrikarddaniel
erikrikarddaniel approved these changes Aug 22, 2025
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Looks all good, although, IIRC, I had to do the Math.floor() and Math.max() things in bbmap/align to make sure I got an integer rounded down and that I never got a 0.

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bbmap/align currently has what's implemented in this PR.
See https://github.com/nf-core/modules/blob/3351c212144fc8aab0e595165bf447ebecfebd8a/modules/nf-core/bbmap/align/main.nf#L48C1-L48C40

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erikrikarddaniel commented Aug 22, 2025 •
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Correct. I'm mixing up the modules. The one I meant is bbmap/bbnorm: https://github.com/nf-core/modules/blob/48ca3de1737b0144aa9fe05bea2b681f0ae45a95/modules/nf-core/bbmap/bbnorm/main.nf#L28-L42

And, again, the Math.round() must be redundant.

@jfy133 jfy133 merged commit 9e18b4d into dev Aug 22, 2025
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@jfy133 jfy133 deleted the update-bbduk-memory branch August 22, 2025 07:48
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

@mahesh-panchal mahesh-panchal mahesh-panchal approved these changes

@sofstam sofstam Awaiting requested review from sofstam sofstam is a code owner

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee LilyAnderssonLee is a code owner

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Process BBMAP_BBDUK uses float values on maxmem resulting in JVM error

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