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Nextflow 26.08.0-edge

Feature updates and improvements​

Language features​

  • Added an agent primitive to run AI agents as first-class Nextflow tasks by @pditommaso in #7477
  • Added syntax error reporting for an unexpected character in a gstring by @bentsherman in #7353
  • Updated the formatter to preserve comments by @ewels in #7346

Configuration​

  • Added the seqera.executor.maxCpusPerUser config option by @jonmarti in #7367
  • Added the singularity.resourceLimits config option by @bentsherman in #7352
  • Split CLI config handling out of ConfigBuilder by @bentsherman in #7373

S3​

  • Dropped transient object tags when publishing files to S3 by @pditommaso in #7344

Kubernetes​

  • Treated a missing k8s config scope as an empty one by @pditommaso in #7452

Plugins​

  • Aligned the Seqera executor maxSpotAttempts and Fusion handling by @pditommaso in #7412
  • Bounded Seqera executor scheduler requests with a request timeout by @pditommaso in #7466
  • Stopped fabricating a memory request for the Seqera executor by @pditommaso in #7488
  • Used the Platform user identity for the Seqera executor userName label by @pditommaso in #7413
  • Used registry config for plugin repos by @jorgee in #7180

General​

  • Accepted the http requesting protocol for HTTPS proxy CONNECT tunnel authentication by @bentsherman in #7369
  • Added --console=plain to Gradle commands in the Makefile by @pditommaso in #7400
  • Added componentName to the module view command output by @pditommaso in #7385
  • Added a note about AI co-authorship to CLAUDE.md by @bentsherman in #7357
  • Added smolvm container engine support by @pditommaso in #7386
  • Added support for authenticated forward HTTP/HTTPS proxies across the client stack by @pditommaso in #7331
  • Aligned the build to the Java 25 toolchain, targeting Java 17 via --release by @pditommaso in #7370
  • Cached the task context for exec tasks by @pditommaso in #7499
  • Documented the exit logic in the task wrapper script by @bentsherman in #7290
  • Honored COLUMNS when determining ANSI output width by @Eldergenix in #7144
  • Pre-pulled the integration tests container by @pditommaso in #7432
  • Refactored HubOptions from a trait into a record by @bentsherman in #7372
  • Removed dead SpuriousDeps.cmdCloud reflection by @bentsherman in #7371
  • Reported the task directives read while the command is rendered by @bentsherman in #7506
  • Separated the CLI from the runtime by @bentsherman in #5971
  • Updated the CI bucket to s3://nextflow-oss-ci by @bentsherman in #7440
  • Used the WireMock self-contained distribution in nf-tower by @pditommaso in #7485
  • Used command -v instead of which in the launcher Java lookup by @pditommaso in #7433

Dependencies​

  • Bumped Groovy 4.0.33 by @pditommaso in #7429
  • Bumped Netty and Apache HttpComponents to patched releases by @pditommaso in #7484
  • Updated the docs site dependencies to patched releases by @pditommaso in #7486

Bug fixes​

Language features​

  • Fixed a function call in a process directive value with the v2 parser by @bentsherman in #7374
  • Fixed lint reporting of excluded paths by @bentsherman in #7354
  • Fixed a parameterized type cast in a process body by @bentsherman in #7382
  • Fixed a variable incorrectly resolved to an included function name by @bentsherman in #7358

Configuration​

  • Fixed config rendering of nested closures by @bentsherman in #7375
  • Fixed plugin blocks incorrectly merged in the v2 config parser by @bentsherman in #7350

Azure​

  • Fixed detection of Azure virtual directories without a trailing slash by @adamrtalbot in #6428

Wave​

  • Fixed a spurious 'Unrecognized config option' warning for wave.build.compression and wave.build.conda by @pditommaso in #7355

General​

  • Fixed cache invalidation for module binaries by @FloWuenne in #6914
  • Fixed independently-verified findings from a security audit by @ewels in #7503
  • Fixed a negative duration error on a short run by @bentsherman in #7351
  • Fixed the PBS Pro server status query by @jscgh in #7366
  • Fixed the publish mode override when re-publishing an existing file by @bentsherman in #7364
  • Fixed a race condition calling workflow onComplete twice by @bentsherman in #7349
  • Fixed tests failing on macOS and on hosts with NXF_REGISTRY_TOKEN by @pditommaso in #7457
  • Fixed workflow metadata when failOnIgnore is true by @ehsanestaji in #7356
  • Guarded the trace log against string formatting errors by @bentsherman in #7347
  • Prevented a world-readable race window when storing local secrets by @aknownuser in #7307
  • Reverted the stream swap after the redirect to .command.out and .command.err by @tcezard in #7300

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.08.0-edge

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