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Nextflow 25.09.0-edge

Nextflow

Feature updates and improvements​

  • Added listDirectory traversal API to RepositoryProvider abstraction by @pditommaso in #6430
  • Added step to claim plugin in Gradle plugin migration docs by @christopher-hakkaart in #6450
  • Added support for comma-separated file paths in ProcessEntryHandler by @pditommaso in #6434
  • Added support for Java 25 by @pditommaso in #6419
  • Added unit test for invalid workflow entry name error handling by @pditommaso in #6409
  • Generated plugin spec by @bentsherman in #6361
  • Updated Gradle build system to version 9.1.0 by @pditommaso in #6418
  • Bumped Google Cloud libraries to latest versions by @pditommaso in #6438
  • Bumped nextflow-gradle-plugin version 1.0.0-beta.10 by @pditommaso in 812ed7f
  • Bumped nf-amazon@3.3.0 by @pditommaso in 3561c26
  • Bumped nf-azure@1.20.1 by @pditommaso in fae3c2d
  • Bumped nf-codecommit@0.5.0 by @pditommaso in 91514a6
  • Bumped nf-google@1.23.1 by @pditommaso in 153745a
  • Bumped nf-k8s@1.2.1 by @pditommaso in c4f4eca
  • Bumped nf-tower@1.16.0 by @pditommaso in ef91104
  • Bumped nf-wave@1.16.0 by @pditommaso in be01d3f

Bug fixes​

  • Fixed cache command to check session cloudCachePath by @pditommaso in a88e2cd
  • Fixed cache command to use SysEnv for cloudcache path check by @pditommaso in #6432
  • Fixed cookie policy for Seqera Platform JWT token refresh by @pditommaso in #6411
  • Fixed CVE-2025-55163 in nf-google plugin by @pditommaso in 7d70617
  • Fixed default fields in trace config by @bentsherman in #6403
  • Fixed pod log warning with Fusion enabled by @jorgee in #6449
  • Fixed SIGTERM forwarding in AWS Batch jobs by @jorgee in #6414
  • Fixed "Strings must not be null" error message by @bentsherman in #6404
  • Fixed unstage controls in command.run when using storeDir by @jorgee in #6364
  • Limited S3 concurrent downloads to fix Java Heap OOM by @jorgee in #6402
  • Got exit code from pod to manage OOM in k8s by @jorgee in #6442

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.09.0-edge