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Changelog

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

Wave v1.30.0

Wave

Feature updates and improvements​

  • Added configurable Singularity init container image by @pditommaso in #937
  • Used Seqera-hosted buildkit image by @pditommaso in #938
  • Added labels in ConfigSpec by @munishchouhan in #934

Bug fixes​

  • Fixed typos in Wave Kubernetes install by @christopher-hakkaart in #930
  • Fixed scan and mirror enabled flag bug by @munishchouhan in #935
  • Fixed wave.scan.enabled feature flag and YAML indentation by @pditommaso in #936

Full changelog: https://github.com/seqeralabs/wave/compare/v1.29.1...v1.30.0

Seqera Cloud v25.3.0_cycle33

Seqera Cloud

Feature updates and improvements​

Studios​

  • Updated the Add Studio page to a single-step form.

Compute environments​

  • AWS Batch compute environments now use AmazonLinux2023-based AMIs by default, offering improved security (IMDSv2), better performance with gp3 EBS volumes, and a more recent kernel. Existing compute environments continue to function with AmazonLinux2 without changes, though we recommend migrating to newer compute environments before AmazonLinux2 reaches end-of-life in June 2026.

Bug fixes​

Compute environments​

  • Fixed compute environment variables created without specifying a target environment (head or compute), which prevented the system from applying variables during workflow execution. The system now validates that at least one target environment is specified, preventing invalid configurations and providing clear error messages.

Pipelines​

  • Fixed display issues with long helper text in pipeline schema forms. Helper text now wraps properly within form controls, improving readability for parameter descriptions with technical specifications or long value lists.

Seqera Cloud v25.3.0_cycle32

Seqera Cloud

Bug fixes​

Launchpad​

  • Fixed an empty launch form issue when launching shared pipelines from another workspace. The launch form now correctly retrieves and displays all pipeline configuration when launching shared pipelines across workspaces.

General​

  • Fixed OIDC authentication errors with spaces or special characters that caused application crashes instead of displaying proper error messages. Authentication errors during login now display correctly to users, preventing application failures.

Fusion v2.5.7

Fusion

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.7-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.7-arm64.json'.

Critical bug fixes​

GCS compose conflicts

  • Fixed concurrent compose operation conflicts in Google Cloud Storage.
  • When multiple Fusion instances compose the same target file concurrently (e.g., with Nextflow job arrays where all array jobs overwrite .exitcode), temporary objects created during composition could conflict.
  • Prevents conflicts when concurrent instances attempt to create, use, or delete the same temporary files.

Upgrade notes​

Drop-in replacement for v2.5.x. No configuration changes required.

Fusion v2.5.6

Fusion

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.6-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.6-arm64.json'.

Feature updates and improvements​

  • GPU Usage Monitoring
    • New fusion-gpu-checker utility for monitoring GPU usage by processes.
    • Optional integration via environment variables.
  • GCP Batch support
    • Added support for Google Batch with Fusion Snapshots 1.7.0.
  • Bumped golangci-lint-action: 8.0.0 → 9.0.0
  • Bumped actions/upload-artifact: 4.6.2 → 5.0.0
  • Bumped actions/download-artifact: 5.0.0 → 6.0.0
  • Bumped astral-sh/setup-uv: 6 → 7

Critical bug fixes​

Azure Directory detection

  • Fixed "Is a directory" errors in hierarchical namespace containers (Data Lake Gen2).
  • Fixed files incorrectly treated as directories causing workflow failures.

Context cancellation

  • Fixed critical operations failing mid-execution due to FUSE context cancellation.
  • Prevented data corruption, ghost files, and orphaned S3 objects.
  • Operations now complete reliably despite client disconnections.

Symlink compaction deadlocks

  • Fixed deadlock in entryService shutdown with symlink compaction.
  • Ensured target directory population before compaction.

Other improvements​

Reliability

  • Fixed race condition in directory iteration.
  • Fixed write lock acquisition condition reevaluation.
  • Added comprehensive lock documentation.

Testing and CI

  • Pinned Nextflow to 25.04.8.
  • Updated license test certificates (40-year expiration).
  • Added GPU tracer test coverage.

Upgrade notes​

Drop-in replacement for v2.5.x. No configuration changes required.

Seqera Cloud v25.3.0_cycle31

Seqera Cloud

Feature updates and improvements​

Data Explorer​

  • Added support for LakeFS Cloud in Data Explorer by enabling image preview and file upload functionality when using LakeFS Cloud as an S3-compatible storage provider.

Compute environments​

  • Improved job failure handling in AWS Batch compute environments. Improved AWS Batch workflow behavior to automatically terminate unschedulable jobs instead of leaving them pending indefinitely, providing faster feedback when compute resources are insufficient for workflow requirements.
  • Added the g6e instance family to the list of AWS instances with NVMe storage.

Bug fixes​

Workflows​

  • Fixed an issue where plots and charts in MultiQC reports appeared as grey boxes instead of displaying correctly, ensuring all visualizations now render properly. MultiQC reports generated by pipeline runs now display complete quality control metrics and interactive charts without missing content.

Studios​

  • Fixed an issue where YAML validation errors did not display immediately when importing Studio configurations from Git repositories, ensuring configuration issues are now visible as soon as the import completes.

Compute environments​

  • Fixed an issue where AWS single VM compute environments could not pull container images from private Amazon ECR repositories, bringing them to feature parity with AWS Batch compute environments.

Launchpad​

  • Fixed an issue with older pipeline launch records, where the system did not set the source type properly, resulting in the system failing to access the pipeline entity on launch.