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fix: CLIN-3453 add missing resources for exomiser process in config #51

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LysianeBouchard
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@LysianeBouchard LysianeBouchard commented Dec 18, 2024

This pull request adds default resource values for the exomiser process. The values are based on realistic exomiser reference data used in the QLIN environment.

While it may be possible to reduce resource requirements when using fewer exomiser data sources, we aim to provide defaults that are likely to work in most cases. These defaults should give users a good idea of the requirements for a production deployment.

Tests

Run the pipeline locally:
nextflow run main.nf -profile test,docker

Juno Tests

Run the pipeline in Juno. Check that the allocated resources on the exomiser pod are matching the configuration.

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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.
  • Reference Data Documentation in docs/reference_data.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@LysianeBouchard LysianeBouchard marked this pull request as draft December 18, 2024 03:44
@LysianeBouchard LysianeBouchard force-pushed the fix/CLIN-3452-add-missing-resources-for-exomiser-process-in-config branch 4 times, most recently from be9d8ff to c13bc35 Compare December 18, 2024 15:47
@LysianeBouchard LysianeBouchard force-pushed the fix/CLIN-3452-add-missing-resources-for-exomiser-process-in-config branch from c13bc35 to 2af0e07 Compare December 18, 2024 15:48
@LysianeBouchard LysianeBouchard marked this pull request as ready for review December 18, 2024 16:36
@LysianeBouchard LysianeBouchard merged commit 309507f into main Dec 18, 2024
3 checks passed
@LysianeBouchard LysianeBouchard deleted the fix/CLIN-3452-add-missing-resources-for-exomiser-process-in-config branch December 18, 2024 16:43
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2 participants