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Nextflow 25.11.0-edge

Nextflow

Feature updates and improvements​

  • Add Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in #6431
  • Add default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Add test case for printing config with nested includes by @Lehmann-Fabian in #2498
  • Allow pre-existing write-protected plugins directory to be used by @bentsherman in #6594
  • Change log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in #6523
  • Improve error message for invalid accelerator resource by @bentsherman in #6585
  • Improve error message for invalid contribution type in manifest contributors by @bentsherman in #6593
  • Issue templates: add external links via config by @ewels in #6563
  • Move task error formatting logic into separate class by @bentsherman in #6551
  • Optimize exit code handling by relying on scheduler status for successful executions by @jorgee in #6484
  • Remove unnecessary runtime checks with strict syntax by @bentsherman in #6539
  • Remove unused BatchHelper class by @pditommaso in #6547
  • Remove wiremock-groovy dependency and update tests using this dependency by @jorgee in #6611
  • Update bundled Docker runtime to 19.03.15 by @yarikoptic in #6565
  • Update migration timeline for plugin registry by @bentsherman in #6543
  • Update trace table columns in Reports page by @JustinBellavance in #6483
  • Upgrade from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in #6511
  • Add admonition to clarify plugin provider and org by @christopher-hakkaart in #6536
  • Add admonition to inputs and index words by @christopher-hakkaart in #6461
  • Improve task previousTrace documentation by @rnaidu in #6538
  • Mark Fusion.tags as supported only for S3 by @fntlnz in #6601
  • Update feature flags page by @christopher-hakkaart in #6504
  • Update task directives by @christopher-hakkaart in #6506
  • Bump Fusion to version 2.5 by @jordeu in #6557
  • Bump Gradle 9.2.0 by @pditommaso in 2657524
  • Bump groovy 4.0.29 by @pditommaso in #6510
  • Bump logback to version 1.5.20 by @pditommaso in 462eec5
  • Bump org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 by @dependabot in #6537
  • Bump nf-amazon@3.5.0
  • Bump nf-azure@1.21.0
  • Bump nf-google@1.24.0
  • Bump nf-k8s@1.3.0
  • Bump nf-tower@1.18.0
  • Bump nf-wave@1.17.0

Bug fixes​

  • Fix Do not delete K8s jobs when ttlSecondsAfterFinished is set by @bentsherman in #6597
  • Fix Fusion license JWT token refresh by reusing TowerClient by @jorgee in 498125d
  • Fix Invalid type error detection by @pditommaso in 9e3aeed
  • Fix K8sTaskHandlerTest method name typos by @pditommaso in bcf81d9
  • Fix asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605
  • Fix csv splitter when skipping empty lines by @bentsherman in #6586
  • Fix documentation of unique operator by @bentsherman in #6541
  • Fix error with dynamic directives with named arguments by @bentsherman in #6550
  • Fix false config validation warnings for process selectors by @bentsherman in #6542
  • Fix false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fix incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fix invalid cache write when cacheable split operation fails by @bentsherman in #6588
  • Fix issue with optional workflow output by @bentsherman in #6519
  • Fix issues with rsync stage-out mode by @bentsherman in #6587
  • Fix security vulnerabilities in org.json dependency by @pditommaso in c7161c2
  • Fix unordered completed parts in AWS multipart upload by @jorgee in #6560
  • Fix TowerJsonGenerator thread-safety issue by @pditommaso in #6619
  • Fix Plugins.init() in run command to original location by @jorgee in #6568
  • Fix security vulnerabilities for wiremock by @jorgee in #6607
  • Fix replace complete plotly bundle with smaller more specific one by @mashehu in #6527
  • Fix stageFileEnabled flag to control .command.stage file creation by @pditommaso in #6618

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.11.0-edge