v1.0.0-rc12

ℹ️ This is a release candidate for the first production release (v1.0.0) of the GPS Pipeline
ℹ️ This version of the pipeline has been validated by 21K samples from the GPS Database published data

The GPS Pipeline is now in preprint! 🎉
Please cite this pipeline if you have used it in your work: https://doi.org/10.1101/2024.11.27.625679 [Preprint]

What's Changed (since v1.0.0-rc11)

Changes

• Update to SeroBA 2.0.4 (#137): Predict 102 of 107 known pneumococcal serotypes, 16 subtypes in selected serotypes, and 4 groups of non-encapsulated pneumococci
• Update Nextflow to 24.10.3 (#140): Compatible with the latest version of Nextflow

Fixes

• Fail the PBP_RESISTANCE process if spn_pbp_amr generates empty output (#138): As spn_pbp_amr should not generate empty output, the process will be properly considered as fail if it does.
• Cap maximum thread usage to samtools sort due to diminishing return and to avoid excessive memory request (#139): As samtools sort assigns memory per thread and there is a diminishing return beyond 8 threads, it will no longer use more than 8 threads to avoid edge cases where a machine has high thread count but only limited memory available crashing the tool

Full Changelog: v1.0.0-rc11...v1.0.0-rc12