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Fusion v2.5.5

How to pin this version​

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

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.5-arm64.json'.

Feature updates and improvements​

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

Snapshots​

  • GCP Snapshot support: Add Google Batch (GCP) support for snapshots with comprehensive compute environment detection and metadata client integration.
  • Snapshot version: Bump fusion-snapshot to v1.7.0 with GCP support.

Configuration​

  • Locking documentation: Add comprehensive lock documentation to entryService including invariants, lock upgrade patterns, and TOCTOU prevention.
  • 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.

Dependencies​

  • 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​

General​

  • 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.

MultiQC v1.32

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.

Nextflow 25.10.0

Feature updates and improvements​

Language features​

  • Added type checking utils by @bentsherman in #6482

Google Batch​

  • Prioritized Google Batch API exit codes with fallback to .exitcode file by @jorgee in #6498

S3​

  • Simplified S3 configuration options by @bentsherman in #6496

General​

  • Added publish-artifacts step to release process by @pditommaso in 75d8ebf
  • Showed workspace roles in 'auth status', tweaked error message on 403 by @ewels in #6497
  • Tracked remote input files in lineage by @jorgee in #6490

Dependencies​

  • 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​

AWS Batch​

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

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

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