Changelog

Feature updates and improvements​

• Added CRAN package support for Wave container builds by @pditommaso in #874

Full changelog: https://github.com/seqeralabs/wave/compare/v1.27.0...v1.28.0

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.17-amd64.json'
}

Feature updates and improvements​

• Fixed lock with symlink compaction.

Feature updates and improvements​

Datasets​

• Added support for date-only formats in search queries, allowing you to search using simple dates (e.g., 2025-02-02) instead of full ISO-8601 datetime strings.

Pipelines​

• Added pipeline version numbers and descriptions to preconfigured onboarding pipelines, making it easier to understand what each pipeline does.

Bug fixes​

Data Explorer​

• Fixed an issue where filtering for Azure credentials in Data Explorer only returned one credential type instead of all three available Azure credential types.
• Fixed an issue where the Data Explorer link did not appear in Task View when configuring multiple AWS credentials with similar permissions in the workspace.

Compute environments​

• Fixed an issue where Seqera Compute environments did not apply proper EC2 instance type constraints, ensuring consistent compute environment behavior and preventing instance unavailability issues.

Launchpad​

• Fixed an issue where users could dismiss critical notifications about compute environment substitutions when relaunching pipelines, ensuring important status messages remain visible throughout the workflow.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.16-amd64.json'
}

Feature updates and improvements​

• Added Google Batch (GCP) support for snapshots.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.5-amd64.json'
}

Feature updates and improvements​

Release v2.5.5 with GCP snapshot support, critical race condition fixes, dependency updates, and improved reliability.

• GCP Snapshot support: Add Google Batch (GCP) support for snapshots with comprehensive compute environment detection and metadata client integration.
• Locking documentation: Add comprehensive lock documentation to entryService including invariants, lock upgrade patterns, and TOCTOU prevention.
• Snapshot version: Bump fusion-snapshot to v1.7.0 with GCP support.
• Preemption handling: Improve logging and handling of instance reclamation/spot termination events.
• Nextflow pinning: Pin Nextflow to 25.04.8 in CI to work around AWS authentication issues in 25.10.0.
• Bumped AWS SDK v2 components (1.19.11 → 1.19.13, 1.88.3 → 1.88.5, etc.)
• Bumped Azure SDK for Go (1.6.2 → 1.6.3, azidentity 1.12.0 → 1.13.0)
• Bumped Google APIs (0.251.0 → 0.252.0)
• Bumped golang.org/x/sys (0.36.0 → 0.37.0)
• Bumped failsafe-go (0.9.0 → 0.9.1)

Critical fixes​

• Race Condition Fixes:
  • Resolve multiple race conditions in entry service operations.
  • Fix directory iteration race by consolidating lock scope.
  • Add lock condition re-evaluation after write lock acquisition to prevent TOCTOU issues.
• Priority test reliability: Improve TestBandwidthExecutor/PriorityExecution statistical reliability by increasing buffer and task counts.
• Directory operations: Ensure rmdir() properly fails on non-empty directories.
• License tests: Update test certificates to expire in 40 years (2065) to prevent test failures.

The MultiQC v1.32 release features one major change:

• Bootstrap upgrade and DARK MODE (#3264)

This has been brewing for a long time, and is a large rewrite of how MultiQC HTML / CSS and JS is written and packaged.

MultiQC now supports simple theming with Bootstrap color modes, and the updated default template ships with both light- and dark-mode by default 😎.

The old template is still available, but has been renamed to original.

Feature updates and improvements​

• Updated Wave use cases and FAQ by @christopher-hakkaart in #917
• Upgraded Netty to 4.2.5. final to fix CVE-2025-58057 by @jordeu in #920
• Refactored MoshiEncodeStrategy to remove Wave-specific polymorphic type adapters by @pditommaso in #922

Full changelog: https://github.com/seqeralabs/wave/compare/v1.26.0...v1.26.1

Feature updates and improvements​

• Added publish-artifacts step to release process by @pditommaso in 75d8ebf
• Added type checking utils by @bentsherman in #6482
• Prioritized Google Batch API exit codes with fallback to .exitcode file by @jorgee in #6498
• Showed workspace roles in 'auth status', tweaked error message on 403 by @ewels in #6497
• Simplified S3 configuration options by @bentsherman in #6496
• Tracked remote input files in lineage by @jorgee in #6490
• Bumped nf-amazon@3.4.1 by @pditommaso in 0d5ced9
• Bumped nf-google@1.23.3 by @pditommaso in e6c7652
• Bumped nf-tower@1.17.1 by @pditommaso in 2069c97

Bug fixes​

• Fixed no secrets in AWS Batch jobs by @jorgee in #6499

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.0

Feature updates and improvements​

• Added .command.log redirection in K8s container command by @jorgee in #6455
• Added nextflow auth command for Seqera Platform authentication by @pditommaso in #6463
• Added nextflow launch command by @jorgee in #6491
• Brought workflow outputs out of preview by @bentsherman in #6487
• Improved plugin create confirmation prompt by @robsyme in #6473
• Improved release script validation by @pditommaso in 3e3a938
• Limited S3 client connections when using virtual threads by @jorgee in #6369
• Migrated SraExplorer to use HxClient for HTTP operations by @pditommaso in #6467
• Renamed config.schema package to config.spec by @bentsherman in #6485
• Typed processes by @bentsherman in #6368
• Updated buildInfo on releaseInfo by @pditommaso in 46a8a2b

Bug fixes​

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

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.