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Nextflow 26.09.0-edge

Feature updates and improvements​

Language features​

  • Added direct execution of named workflows by @jorgee in #7379
  • Added workflow modules by @bentsherman in #7342
  • Deprecated the storeDir directive and documented an alternative approach by @bentsherman in #7574
  • Documented multiple architectures in the arch directive by @pditommaso in #7622
  • Made eval output names stable across runs by @bentsherman in #7575
  • Reported a syntax error for an invalid output or emit assignment by @bentsherman in #7547
  • Reported an error for an aliased type include by @bentsherman in #7557
  • Reported invalid escape sequences at the exact position by @bentsherman in #7608

Configuration​

  • Added a directory option to resolve report paths against outputDir by @bentsherman in #7553
  • Added the manifest.diagram config option by @pinin4fjords in #7578

Azure​

  • Added Azure Compute Gallery image and verification options by @LennyBEL in #7338

Google Batch​

  • Sped up submission of Google Batch array jobs by @thalassemia in #6847

Kubernetes​

  • Changed the default k8s compute resource type to Job by @bentsherman in #7524

Plugins​

  • Added extension points for task caching and object-storage access by @jorgee in #7638
  • Removed support for nf-weblog by @bentsherman in #7639

General​

  • Added automatic resource labels for any executor by @pditommaso in #7528
  • Added a codespell CI check and fixed existing typos by @ewels in #7594
  • Added configurable timeouts to SCM API requests by @robsyme in #7536
  • Added deep links to migration notes by @bentsherman in #7624
  • Added retries for request timeouts in the Tower and Wave HTTP clients by @pditommaso in #7604
  • Adopted the shared io.seqera:lib-util-net ProxyConfig for egress proxy handling by @pditommaso in #7587
  • Cleaned local task directories in hybrid runs by @bentsherman in #7611
  • Cleaned up ADR prose and fixed typos by @bentsherman in #7595
  • Cleaned up the 26.08.0-edge changelog by @pditommaso in #7527
  • Deduplicated include URI resolution logic by @bentsherman in #7644
  • Improved resilience to delayed shared file system visibility by @pditommaso in #7489
  • Made NXF_AGENT_MODE an explicit override of agent mode auto-detection by @bentsherman in #7615
  • Renamed SCM HTTP client timeouts to the global NXF_HTTPCLIENT_* namespace by @pditommaso in #7567
  • Stopped Nextflow submitting queued tasks after the session has aborted by @Mohit-Ak in #7482

Dependencies​

  • Aligned the nf-agent test Groovy dependency to 4.0.33 by @pditommaso in #7559
  • Fixed Jackson, Netty, and gRPC CVEs via API-scoped dependency constraints by @jorgee in #7329

Bug fixes​

Language features​

  • Fixed cloning of typed process outputs to also clone topics by @bentsherman in #7556
  • Fixed formatting of legacy type annotations by @bentsherman in #7525

Configuration​

  • Fixed a false warning for executor selectors by @bentsherman in #7555
  • Fixed the description for process config options with method overloads by @bentsherman in #7442
  • Fixed the resume config breaking other CLI commands by @bentsherman in #7581

S3​

  • Fixed S3 directory upload skipping symbolic links by @jorgee in #7515
  • Fixed workflow output publishing to S3 with the default path by @bentsherman in #7518

Azure​

  • Fixed nf-azure plugin tier-1 bugs by @adamrtalbot in #6831

Google Batch​

  • Fixed nextflow clean aborting on GCS pseudo-directories by @bentsherman in #7630
  • Fixed the env config scope not applied with Google Batch by @bentsherman in #7609
  • Fixed Google Batch storing symlinked task outputs as gcsfuse placeholders by @bentsherman in #7612

Plugins​

  • Fixed resolution of non-core plugin dependencies from the registry by @bentsherman in #7613

General​

  • Fixed a typo in the error message for an invalid LID path by @ewels in #7593
  • Fixed the lineage checksum computed in standard mode regardless of label by @bentsherman in #7582
  • Fixed a local executor resource accounting race by @pditommaso in #7652
  • Fixed the multi-revision test failing locally by @bentsherman in #7541
  • Fixed the output index file write to object storage by @bentsherman in #7635
  • Improved NFS lock error handling in DefaultCacheStore by @matthdsm in #6997

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.0-edge

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