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Nextflow 25.11.0-edge

Nextflow

Feature updates and improvements​

  • Added Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in #6431
  • Added default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Added test case for printing config with nested includes by @Lehmann-Fabian in #2498
  • Allowed pre-existing write-protected plugins directory to be used by @bentsherman in #6594
  • Changed log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in #6523
  • Improved error message for invalid accelerator resource by @bentsherman in #6585
  • Improved error message for invalid contribution type in manifest contributors by @bentsherman in #6593
  • Added external links via config by @ewels in #6563
  • Moved task error formatting logic into separate class by @bentsherman in #6551
  • Optimized exit code handling by relying on scheduler status for successful executions by @jorgee in #6484
  • Removed unnecessary runtime checks with strict syntax by @bentsherman in #6539
  • Removed unused BatchHelper class by @pditommaso in #6547
  • Removed wiremock-groovy dependency and updated tests using this dependency by @jorgee in #6611
  • Updated bundled Docker runtime to 19.03.15 by @yarikoptic in #6565
  • Updated migration timeline for plugin registry by @bentsherman in #6543
  • Updated trace table columns in Reports page by @JustinBellavance in #6483
  • Upgraded from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in #6511
  • Added admonition to clarify plugin provider and org by @christopher-hakkaart in #6536
  • Added admonition to inputs and index words by @christopher-hakkaart in #6461
  • Improved task previousTrace documentation by @rnaidu in #6538
  • Marked Fusion.tags as supported only for S3 by @fntlnz in #6601
  • Updated feature flags page by @christopher-hakkaart in #6504
  • Updated task directives by @christopher-hakkaart in #6506
  • Bumped Fusion to version 2.5 by @jordeu in #6557
  • Bumped Gradle 9.2.0 by @pditommaso in 2657524
  • Bumped groovy 4.0.29 by @pditommaso in #6510
  • Bumped logback to version 1.5.20 by @pditommaso in 462eec5
  • Bumped org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 by @dependabot in #6537
  • Bumped nf-amazon@3.5.0 by @pditommaso in 17cc2b0
  • Bumped nf-azure@1.21.0 by @pditommaso in 0b56d2a
  • Bumped nf-google@1.24.0 by @pditommaso in 81a5a05
  • Bumped nf-k8s@1.3.0 by @pditommaso in 7146011
  • Bumped nf-tower@1.18.0 by @pditommaso in 86da3b7
  • Bumped nf-wave@1.17.0 by @pditommaso in de02e8b

Bug fixes​

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