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fgbio: scale JVM heap with task.memory - #13684

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WEHIGenomicsRnD:fgbio-jvm-mem-fix
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mcmero wants to merge 1 commit into
nf-core:masterfrom
WEHIGenomicsRnD:fgbio-jvm-mem-fix

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@mcmero mcmero commented Nov 11, 2026

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Closes #13627.

mem_gb started at 8 and was only ever lowered, so tasks given more than 8 GB still ran with -Xmx8g. Set it to task.memory.giga - 1 (minimum 1), falling back to 8 when memory is unknown. CallMolecularConsensusReads previously used the full allocation with no headroom and now leaves 1 GB.

Also fix the log label in groupreadsbyumi, which named FilterConsensusReads.

Generated by Claude Code

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

mem_gb started at 8 and was only ever lowered, so tasks given more than
8 GB still ran with -Xmx8g. Set it to task.memory.giga - 1 (minimum 1),
falling back to 8 when memory is unknown. callmolecularconsensusreads
previously used the full allocation with no headroom and now leaves 1 GB.

Also fix the log label in groupreadsbyumi, which named FilterConsensusReads.

Generated by Claude Code

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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fgbio modules cap JVM heap size to 8GB

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