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Changelog

Fusion v2.5.4

Fusion

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.4-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.4-arm64.json'.

Feature updates and improvements​

  • Added support for checksum algorithm.
  • Added incremental dumps.
  • Added ability to disable OTEL machinery if tracing not enabled.
  • Added fallback to use AZ_BATCH_TASK_WORKING_DIR as FUSION_CACHE_LOCATION.
  • Updated fusion snapshots to 1.6.0
  • Bumped github.com/docker/docker from 28.2.2+incompatible to 28.3.3+incompatible
  • Bumped hoverkraft-tech/compose-action from 2.3.0 to 2.4.0
  • Bumped google.golang.org/grpc from 1.75.0 to 1.75.1
  • Bumped actions/download-artifact from 4.3.0 to 5.0.0
  • Bumped insightsengineering/coverage-action from 2.7.2 to 3.0.1

Nextflow 25.09.0-edge

Nextflow

Feature updates and improvements​

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

Bug fixes​

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

Seqera Cloud v25.3.0_cycle27

Seqera Cloud

Feature updates and improvements​

  • Platform
    • Enhanced dataset management with an updated details page.
    • Added the ability to hide/show datasets and disable specific dataset versions for better dataset lifecycle management.
    • Added support for dataset labels to improve organization and categorization of datasets within workspaces.
    • Added the ability to filter pipeline runs by dataset ID using the datasetId: search keyword, improving traceability between datasets and workflows.

Bug fixes​

  • Fixed an issue where errors for deleted or invalid pipeline revisions appeared on the wrong field, making them difficult to identify and resolve.

Seqera Enterprise v25.2.3

Seqera Enterprise

Feature updates and improvements​

  • Studios
    • Added three new configuration parameters for customizing Docker image naming conventions in Studios Wave integration.
    • Added eStarGZ support for Studios with conda packages.
  • Platform
    • Introduced multiple improvements to the Usage Overview to simplify compute usage tracking.
    • Added automatic memory tracking for billing to automatically capture actual memory usage for tasks without explicit memory limits, ensuring accurate consumption tracking.
  • Pipelines
    • The progress response now includes retries and ignored status task counts when a workflow is finalized.
    • Improved loading time for pipeline details (up to 700ms improvement) for repositories like nf-core/rnaseq. This resolves timeout issues when launching pipelines.

Bug fixes​

  • Fixed a missing newline in the includeCustomUserConfig method and resolved an issue where where custom config includeConfig statements were improperly concatenated, causing syntax errors when parsed.

Seqera Cloud v25.3.0_cycle25

Seqera Cloud

Feature updates and improvements​

  • Fusion
    • Added FSx Lustre support for Amazon Linux 2023 AMIs with automatic fallback from the Amazon Linux 2 installation method.
  • Platform API
    • Added an optional maxLength query parameter to workflow log endpoints (GET /{workflowId}/log and GET /{workflowId}/log/{taskId}) for improved log management.
    • Added the managed identity and managed credentials endpoint to Seqera Platform API documentation.
  • Improved warning messages in Seqera Platform when workflows are cancelled or Studios are stopped due to insufficient credits.
  • Removed the role check to show organization member mail, so organization owners can now view member and collaborator emails.
  • Added user tracking fields to datasets and dataset versions. Datasets now include a lastUpdatedBy field to track the user who last modified the dataset, while dataset versions include a createdBy field to track the user who created each version.
  • Improved the visual consistency and user experience across workflow run interfaces. Updates include improved table borders, enhanced tooltip information, and refined pagination layouts in the containers view.

Wave v1.25.1

Wave

Feature updates and improvements​

  • Removed unused env from jib task definition by @pditommaso in 3471824
  • Replaced deprecated AppArmor annotation with securityContext field by @pditommaso in #896
  • Removed app encoded values for Seqera environment @munishchouhan in #893
  • Bumped BuildKit to version 0.23.2 in tests @munishchouhan in #894
  • Bumped MN to version 4.9.3 by @pditommaso in 03b98e8
  • Bumped BuildKit to version 0.23.2 by @pditommaso in f31316d
  • Bumped corretto-25-al2023-mimalloc as base image by @pditommaso in 46a6e2a

Full changelog: https://github.com/seqeralabs/wave/compare/v1.25.0...v1.25.1

Nextflow 25.08.0-edge

Nextflow

Feature updates and improvements​

  • Add Claude Code GitHub Action integration by @pditommaso in #6389
  • Add Value type for dataflow values (value channels) by @bentsherman in #6372
  • Add descriptions to plugin MANIFEST.MF files by @pditommaso in #6348
  • Add null checks in TowerClient onFlowComplete method by @robsyme in #6384
  • Add plugins redirects by @christopher-hakkaart in #6385
  • Add test for prefetchMetadata call in pullPlugins method by @pditommaso in #6396
  • Add Type annotations by @bentsherman in #6278
  • Implement Process Execution with Command-Line Parameter Mapping [experimental] by @pditommaso in #6381
  • Improve secret loading documentation and rename ConfigNullProvider to EmptySecretProvider by @bentsherman in 9e4c975
  • Minor TowerClient improvement by @pditommaso in #6387
  • New executor for Fujitsu Technical Computing Suite (TCS) by @exthnet in #5928
  • Preserve method parameter names in nf-lang JAR by @bentsherman in #6355
  • Refactor Wave and Tower client to use lib-httpx library by @pditommaso in #6354
  • Replace custom JWT refresh logic with standardized HxClient by @pditommaso in #6398
  • Replace custom retry strategy with HxClient in RepositoryProvider by @pditommaso in #6351
  • Simplify plugin download implementation by @pditommaso in #6349
  • Support standard environment variables for ANSI terminal output by @ewels in #6362
  • Update core plugins to use Nextflow Gradle plugin by @bentsherman in #6379
  • Warn when file() matches a collection of files by @bentsherman in #5507
  • Workflow params by @bentsherman in #5929
  • Bump netty deps to version 4.1.124.Final by @pditommaso in 9e8d596

Bug fixes​

  • Fix CLI param override in strict config parser by @bentsherman in #6377
  • Fix GString equality checks with String by @bentsherman in #6330
  • Fix GitHub Actions commit message parsing to use only first line by @pditommaso in 5bc9162
  • Fix NPE when contributors omit contribution field in manifest by @robsyme in #6383
  • Fix Platform refresh token handling by @pditommaso in ba78ef7
  • Fix duplicate page and redirects in docs by @christopher-hakkaart in #6386
  • Fix false warning for map config options by @bentsherman in #6359
  • Fix groupTuple operator to handle GString vs String keys consistently by @pditommaso in #6400
  • Fix incorrect spelling in docs by @christopher-hakkaart in #6336
  • Fix null reference error in workflow output by @bentsherman in #6374
  • Fix typo in task config eval by @bentsherman in #6392

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.08.0-edge