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Nextflow 25.09.2-edge

Feature updates and improvements​

Language features​

  • Brought workflow outputs out of preview by @bentsherman in #6487
  • Typed processes by @bentsherman in #6368

Kubernetes​

  • Added .command.log redirection in K8s container command by @jorgee in #6455

S3​

  • Limited S3 client connections when using virtual threads by @jorgee in #6369

Plugins​

  • Improved plugin create confirmation prompt by @robsyme in #6473

Configuration​

  • Renamed config.schema package to config.spec by @bentsherman in #6485

General​

  • Added nextflow auth command for Seqera Platform authentication by @pditommaso in #6463
  • Added nextflow launch command by @jorgee in #6491
  • Improved release script validation by @pditommaso in 3e3a938
  • Migrated SraExplorer to use HxClient for HTTP operations by @pditommaso in #6467
  • Updated buildInfo on releaseInfo by @pditommaso in 46a8a2b

Bug fixes​

Language features​

  • Fixed false error with storeDir and val outputs by @bentsherman in #6408

Configuration​

  • Fixed e2e test infrastructure and added config.schema compatibility aliases by @pditommaso in #6495
  • Fixed false error for executor.jobName config option by @bentsherman in #6375

Plugins​

  • Fixed type casting in PluginSpec for ConfigScope by @pditommaso in #6469

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.09.2-edge

Seqera Cloud v25.3.0_cycle28

Feature updates and improvements​

Compute environments​

  • Updated documentation on free credit entitlement and management.
  • Updated the default Seqera AMI version to 0.0.10 for both AMD64 and ARM64 architectures in AWS Cloud deployments.

UI/UX​

  • Added a copy button to data display chips, allowing you to quickly copy displayed values to your clipboard.
  • Added an improved onboarding flow for Seqera Compute customers to quickly run pipelines.

Pipelines​

  • Added support for pinning the HEAD commit ID of the chosen revision to guarantee deterministic pipeline execution.

Data Explorer​

  • Added support for image preview and file upload in Data Explorer when using Amazon S3-compatible API storage (for example, but not limited to, Cloudflare R2, MinIO, and Oracle Cloud).
  • Added support for MinIO object storage in Data Explorer, enabling users to browse, upload, and download files from MinIO instances using S3-compatible credentials.

Workflows​

  • Added the ability to read task logs on Azure Cloud from Azure Blob Storage after pipeline completion, ensuring logs remain accessible throughout the entire task lifecycle.
  • Updated the nf-launcher container versions from 25.04.6 to 25.04.8 for both standard and Docker-in-Docker variants.

Bug fixes​

Pipelines​

  • Fixed an issue where resuming pipelines failed due to incorrect identification of launchable entity types.
  • Fixed issues where version name autogeneration used incorrect defaults and navigation returned users to the wrong page when editing pipeline versions.

Studios​

  • Fixed an issue where users with Launch permissions could not access Studios due to insufficient workspace settings permissions.

General​

  • Fixed an issue where administrators could accidentally create duplicate user accounts due to differences in email address casing.

Fusion v2.4.15

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.15-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.15-arm64.json'.

Feature updates and improvements​

Snapshots​

  • Added incremental dumps on 2.4.
  • Bumped snapshots to 1.6.0 in 2.4.15

Fusion v2.5.4

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​

Snapshots​

  • Added incremental dumps.
  • Updated fusion snapshots to 1.6.0

Configuration​

  • Added support for checksum algorithm.
  • Added ability to disable OTEL machinery if tracing not enabled.
  • Added fallback to use AZ_BATCH_TASK_WORKING_DIR as FUSION_CACHE_LOCATION.

Dependencies​

  • 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

Feature updates and improvements​

Language features​

  • Added support for comma-separated file paths in ProcessEntryHandler by @pditommaso in #6434
  • Added unit test for invalid workflow entry name error handling by @pditommaso in #6409

Plugins​

  • Added step to claim plugin in Gradle plugin migration docs by @christopher-hakkaart in #6450
  • Generated plugin spec by @bentsherman in #6361

General​

  • Added listDirectory traversal API to RepositoryProvider abstraction by @pditommaso in #6430
  • Added support for Java 25 by @pditommaso in #6419
  • Updated Gradle build system to version 9.1.0 by @pditommaso in #6418

Dependencies​

  • 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​

AWS Batch​

  • Fixed SIGTERM forwarding in AWS Batch jobs by @jorgee in #6414

S3​

  • Limited S3 concurrent downloads to fix Java Heap OOM by @jorgee in #6402

Kubernetes​

  • Fixed pod log warning with Fusion enabled by @jorgee in #6449
  • Got exit code from pod to manage OOM in k8s by @jorgee in #6442

Google Cloud​

  • Fixed CVE-2025-55163 in nf-google plugin by @pditommaso in 7d70617

Configuration​

  • Fixed default fields in trace config by @bentsherman in #6403

General​

  • 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 "Strings must not be null" error message by @bentsherman in #6404
  • Fixed unstage controls in command.run when using storeDir by @jorgee in #6364

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

Seqera Cloud v25.3.0_cycle27

Feature updates and improvements​

Datasets​

  • 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.

Workflows​

  • Added the ability to filter pipeline runs by dataset ID using the datasetId: search keyword, improving traceability between datasets and workflows.

Bug fixes​

Pipelines​

  • 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

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.

Workflows​

  • 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.
  • The progress response now includes retries and ignored status task counts when a workflow is finalized.

Pipelines​

  • 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​

Pipelines​

  • 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.