Bug fixes​

Language features​

• Fixed formatter dropping the main: label when onComplete: or onError: is present by @ewels in #7346

General​

• Fixed BitbucketServerRepositoryProvider ignoring the token field by @jorgee in #7120

Dependencies​

• Bumped nf-amazon@3.4.6 by @pditommaso in 30cfdc47

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.8

Feature updates and improvements​

Co-Scientist​

• Made Projects available in organization workspaces to roles with the Projects permission, which existing custom roles don't include.
• Added the Project workspace role, for a user who launches a project's pipelines, adds datasets, and reads run reports from the Projects view, without the workspace's Launchpad, Runs, Datasets, Compute, or Settings pages.
• Added a Projects permission category to custom roles.
• Surfaced proj_ labels as projects in Labels settings.
• Limited the launch picker on a project's Runs tab to pipelines that carry the project's label.

Pipelines​

• Added a Fusion version selector to the launch form, and limited both version lists to compatible versions.

Studios​

• Added Conda packages for custom container images under More settings.
• Shortened the browser tab title on the Studio details and connect pages to Studio: <name>.

Data Explorer​

• Added the bucket versioning state (Enabled, Suspended, Disabled, or Unknown) to the About data repository dialog for Amazon S3 and Google Cloud Storage data repositories.

Data lineage​

• Changed See in Data Explorer on the run Outputs tab to use the output directory from the run's lineage record.

Credentials​

• Added the Set up Workload Identity Federation in GCP panel to Google Workload Identity credentials created from the compute environment form.

Monitoring​

• Added a Quick launch action to the empty runs list.

Bug fixes​

Pipelines​

• Fixed the Add and Update buttons on the action and pipeline forms staying disabled after a pipeline revision failed to load.

Actions​

• Fixed a paused action that names a deleted pipeline being resumable instead of asking you to point it at a live pipeline.

Compute environments​

• Fixed Azure Batch Forge compute environment creation accepting a malformed container registry credential ID, or more than one.

Access control​

• Fixed selecting a template for a custom role not applying its permissions.

General​

• Fixed the Runs and All runs pages showing no results when opened or reloaded with a search filter in the URL.
• Fixed cancelled runs showing an empty Metrics tab.

Fusion v2.6.8 lets Intelligent Compute relaunch a task from a clean start after a failed snapshot restore, and fixes stale file handle errors on idle files in NFS service mode.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.8-amd64.json'
}

Feature updates and improvements​

Fusion Snapshots​

• Added FUSION_SNAPSHOT_CLEAN_START. When it is set, Fusion cleans the work directory and removes leftover snapshot data before the task starts, so a task whose snapshot restore failed can be relaunched from scratch in the same work directory. Intelligent Compute sets it when it relaunches such a task.

Bug fixes​

NFS service mode​

• Fixed files and directories left idle during a task failing with a stale file handle error.

General​

• Fixed a spurious Check available filesystem space error printed every time a mount shut down.

Dependencies​

• Updated test and CI tooling and dependencies.

Upgrade notes​

• Drop-in replacement for v2.6.7. No configuration changes required.
• FUSION_SNAPSHOT_CLEAN_START applies to NFS service mode only, and you do not need to set it yourself. Without it, Fusion behaves as in v2.6.7.
• File handles in NFS service mode stay valid while the Fusion mount keeps running. They do not survive a restart of the mount.

Feature updates and improvements​

Language features​

• Moved the type checker into nf-lang and brought static typing out of preview by @bentsherman in #7656

Google Batch​

• Deprecated Google Batch machine type selection via Cloud Info by @bentsherman in #7677

Plugins​

• Allowed a cache factory to decline a session by @jorgee in #7681

General​

• Added a hint to nextflow log and nextflow clean errors that the commands do not support the cloud cache by @bentsherman in #7676
• Removed a stray git push from the release task by @bentsherman in #7678

Bug fixes​

S3​

• Fixed S3 upload retries by making ByteBufferInputStream resettable by @jorgee in #7577

Google Batch​

• Fixed Google Batch array-child tasks reporting a null machine type by @pditommaso in #7629

Dependencies​

• Bumped Bouncy Castle to 1.85 to fix critical CVEs by @pditommaso in #7658
• Bumped pi-coding-agent to 0.84.4 to fix npm advisories by @pditommaso in #7659
• Bumped slf4j to 2.0.19 by @pditommaso in #7661
• Fixed npm advisories in the docs site dependencies by @pditommaso in #7660
• Bumped nf-agent-pi@0.5.3
• Bumped nf-amazon@3.11.1
• Bumped nf-cloudcache@0.6.2
• Bumped nf-google@1.28.1
• Bumped nf-k8s@1.6.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.1-edge

Feature updates and improvements​

Language features​

• Added direct execution of named workflows by @jorgee in #7379
• Added workflow modules by @bentsherman in #7342
• Deprecated the storeDir directive and documented an alternative approach by @bentsherman in #7574
• Documented multiple architectures in the arch directive by @pditommaso in #7622
• Made eval output names stable across runs by @bentsherman in #7575
• Reported a syntax error for an invalid output or emit assignment by @bentsherman in #7547
• Reported an error for an aliased type include by @bentsherman in #7557
• Reported invalid escape sequences at the exact position by @bentsherman in #7608

Configuration​

• Added a directory option to resolve report paths against outputDir by @bentsherman in #7553
• Added the manifest.diagram config option by @pinin4fjords in #7578

Azure​

• Added Azure Compute Gallery image and verification options by @LennyBEL in #7338

Google Batch​

• Sped up submission of Google Batch array jobs by @thalassemia in #6847

Kubernetes​

• Changed the default k8s compute resource type to Job by @bentsherman in #7524

Plugins​

• Added extension points for task caching and object-storage access by @jorgee in #7638
• Removed support for nf-weblog by @bentsherman in #7639

General​

• Added automatic resource labels for any executor by @pditommaso in #7528
• Added a codespell CI check and fixed existing typos by @ewels in #7594
• Added configurable timeouts to SCM API requests by @robsyme in #7536
• Added deep links to migration notes by @bentsherman in #7624
• Added retries for request timeouts in the Tower and Wave HTTP clients by @pditommaso in #7604
• Adopted the shared io.seqera:lib-util-net ProxyConfig for egress proxy handling by @pditommaso in #7587
• Cleaned local task directories in hybrid runs by @bentsherman in #7611
• Cleaned up ADR prose and fixed typos by @bentsherman in #7595
• Cleaned up the 26.08.0-edge changelog by @pditommaso in #7527
• Deduplicated include URI resolution logic by @bentsherman in #7644
• Improved resilience to delayed shared file system visibility by @pditommaso in #7489
• Made NXF_AGENT_MODE an explicit override of agent mode auto-detection by @bentsherman in #7615
• Renamed SCM HTTP client timeouts to the global NXF_HTTPCLIENT_* namespace by @pditommaso in #7567
• Stopped Nextflow submitting queued tasks after the session has aborted by @Mohit-Ak in #7482

Dependencies​

• Aligned the nf-agent test Groovy dependency to 4.0.33 by @pditommaso in #7559
• Fixed Jackson, Netty, and gRPC CVEs via API-scoped dependency constraints by @jorgee in #7329

Bug fixes​

Language features​

• Fixed cloning of typed process outputs to also clone topics by @bentsherman in #7556
• Fixed formatting of legacy type annotations by @bentsherman in #7525

Configuration​

• Fixed a false warning for executor selectors by @bentsherman in #7555
• Fixed the description for process config options with method overloads by @bentsherman in #7442
• Fixed the resume config breaking other CLI commands by @bentsherman in #7581

S3​

• Fixed S3 directory upload skipping symbolic links by @jorgee in #7515
• Fixed workflow output publishing to S3 with the default path by @bentsherman in #7518

Azure​

• Fixed nf-azure plugin tier-1 bugs by @adamrtalbot in #6831

Google Batch​

• Fixed nextflow clean aborting on GCS pseudo-directories by @bentsherman in #7630
• Fixed the env config scope not applied with Google Batch by @bentsherman in #7609
• Fixed Google Batch storing symlinked task outputs as gcsfuse placeholders by @bentsherman in #7612

Plugins​

• Fixed resolution of non-core plugin dependencies from the registry by @bentsherman in #7613

General​

• Fixed a typo in the error message for an invalid LID path by @ewels in #7593
• Fixed the lineage checksum computed in standard mode regardless of label by @bentsherman in #7582
• Fixed a local executor resource accounting race by @pditommaso in #7652
• Fixed the multi-revision test failing locally by @bentsherman in #7541
• Fixed the output index file write to object storage by @bentsherman in #7635
• Improved NFS lock error handling in DefaultCacheStore by @matthdsm in #6997

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.0-edge

Feature updates and improvements​

Monitoring​

• Added a live task execution timeline to the run Tasks tab, showing each task's queued and running time.

Pipelines​

• Extended the Nextflow version list back to 23.03, from a previous floor of 25.10.
• Added the pipeline diagram declared in manifest.diagram to the launchpad pipeline details page.

Studios​

• Added custom Studio icons, shown in the Studios list and on the Studios page.

Co-Scientist​

• Moved the sandbox chip into the chat composer toolbar, beside the context chips.

Data lineage​

• Made data lineage available in organization workspaces for runs on AWS compute environments.
• Added pipeline:<name> and pipelineId:<id> qualifiers to lineage search, matching a pipeline's runs, tasks, and published files.
• Added pipeline names to lineage search results and a See syntax tips link to the search modal.
• Changed data lineage ingestion from SQS polling to SNS notifications and added s3:ListBucket to the lineage IAM policy; manually configured workspaces must be reconfigured.

General​

• Added the reason an action stopped or failed to the Actions list.
• Redesigned the Actions list as a table showing each action's source, status, last event, and creator, with usage details in a dialog.
• Added guided empty states to list pages, naming the next step to take.

Bug fixes​

Co-Scientist​

• Fixed a closed Co-Scientist chat reopening on page refresh.
• Fixed the left navigation staying collapsed after closing the Co-Scientist chat.

Pipelines​

• Fixed GitHub Redeliver not retrying an action trigger whose launch failed.

Studios​

• Fixed Studios SSH authorization rate limiting applying across all sessions instead of per session.

General​

• Fixed labels beyond the first 100 missing from the launch form and label search, and label assignments dropping selections not on the current page.
• Fixed an unstable sort order that repeated or omitted labels when paging through the label list.

Fusion v2.6.7 fixes a regression introduced in v2.6.6 that stopped retried tasks from starting when Fusion serves a work directory over NFS. If you run v2.6.6 in that configuration, upgrade.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.7-amd64.json'
}

Bug fixes​

NFS service mode​

• Fixed retried tasks timing out with exit code 173 on every host after an interruption.
• Fixed a work directory emptied by an earlier attempt failing to prepare.
• Halved the storage listings needed to prepare a work directory.

Dependencies​

• Updated build tooling and dependencies.

Upgrade notes​

• Drop-in replacement for v2.6.6. No configuration changes required.
• The regression affects Fusion in NFS mode on v2.6.6 only. Earlier v2.6 releases are unaffected.
• Two limitations remain. A work directory reused without being cleaned is not swept, and leftover names can persist there. Snapshot restore in NFS mode is still under active work. Do not assume every restore path is covered.

Fusion v2.6.6 fixes two Fusion Snapshots restore failures and extends Spot reclamation protection for NFS service mode to Google Cloud and Azure.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.6-amd64.json'
}

Bug fixes​

Fusion Snapshots​

• Fixed snapshot restore failing for a task relaunched after its instance was reclaimed.
• Fixed Fusion Snapshots never writing a checkpoint on Google Cloud VMs launched by Intelligent Compute.

NFS service mode​

• Fixed tasks losing their NFS export when a Google Cloud or Azure host was reclaimed.

Dependencies​

• Fixed CI and updated dependencies.

Upgrade notes​

• Drop-in replacement for v2.6.5. No configuration changes required.
• The permissions fix resolves restore failures for a task relaunched after a reclaim. Snapshot restore in NFS mode is still under active work. If you rely on snapshots, do not assume every restore path is covered.

Fusion v2.6.5 fixes Fusion Snapshots restore for a task that is preempted and relaunched, and fixes renamed directories, the storage region lookup, and cache cleanup on unmount.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.5-amd64.json'
}

Bug fixes​

Fusion Snapshots​

• Fixed a relaunched task not finding the checkpoint its previous attempt took.
• Fixed a snapshot missing files from the task work directory in NFS mode.

General​

• Fixed a renamed directory stranding files that were still uploading.
• Added a timeout to the first lookup of a bucket region.
• Fixed mounts never removing their working folder under the cache location.

Dependencies​

• Updated the Go toolchain to 1.27.1.
• Removed dead code and updated CI and dependencies.

Upgrade notes​

• Drop-in replacement for v2.6.4. No configuration changes required.
• The snapshot restore fix covers a task relaunched on a different instance, which is what happens when an instance is reclaimed. A task relaunched against the same still-running Fusion daemon that drained the previous attempt still fails to restore.

Feature updates and improvements​

General​

• Added support for an authenticating egress proxy for outbound HTTP clients via the shared lib-util-net ProxyConfig by @pditommaso in #1125
• Changed env-var-overridable config properties to use kebab-case keys so they can be set from environment variables by @bebosudo in #1096
• Aligned the build toolchain and runtime to Java 25 while keeping the bytecode target at Java 17 by @cristianrcv in #1077
• Allowed the Claude review agent to submit approving PR reviews by @pditommaso in #1105
• Refreshed the self-install documentation by @christopher-hakkaart in #1106

Dependencies​

• Upgraded org.postgresql:postgresql to 42.7.12 (COMP-2149) by @cristianrcv in #1112
• Upgraded io.netty:netty-bom to 4.2.17.Final (COMP-2376) by @cristianrcv in #1135
• Upgraded the jib plugin to 3.5.4 for Java 25 class file support (COMP-2511) by @munishchouhan in #1136
• Updated node dependency to v24.19.0 by @seqeralabs-renovate[bot] in #1111
• Updated node dependency to v24.20.0 by @seqeralabs-renovate[bot] in #1122
• Updated node dependency to v24.21.0 by @seqeralabs-renovate[bot] in #1134
• Updated actions/checkout action to v4.4.0 by @seqeralabs-renovate[bot] in #1103
• Updated actions/checkout action to v6.1.0 by @seqeralabs-renovate[bot] in #1104
• Updated actions/setup-java action to v4.9.1 by @seqeralabs-renovate[bot] in #1108
• Updated actions/setup-java action to v5.7.0 by @seqeralabs-renovate[bot] in #1109
• Updated aws-actions/amazon-ecr-login action to v2.1.6 by @seqeralabs-renovate[bot] in #1102
• Updated aws-actions/amazon-ecr-login action to v2.1.7 by @seqeralabs-renovate[bot] in #1121
• Updated aws-actions/configure-aws-credentials action to v6.2.3 by @seqeralabs-renovate[bot] in #1110
• Updated aws-actions/configure-aws-credentials action to v6.2.4 by @seqeralabs-renovate[bot] in #1127
• Updated docker/login-action action to v4.6.0 by @seqeralabs-renovate[bot] in #1117
• Updated anthropics/claude-code-action action to v1.0.191 by @seqeralabs-renovate[bot] in #1101
• Updated anthropics/claude-code-action action to v1.0.198 by @seqeralabs-renovate[bot] in #1116
• Updated anthropics/claude-code-action action to v1.0.206 by @seqeralabs-renovate[bot] in #1120
• Updated anthropics/claude-code-action action to v1.0.213 by @seqeralabs-renovate[bot] in #1126
• Updated anthropics/claude-code-action action to v1.0.219 by @seqeralabs-renovate[bot] in #1133

Bug fixes​

Container building​

• Fixed Kubernetes builds being reported as failed on Kubernetes 1.36 and later even though the image was built and pushed (COMP-2368) by @munishchouhan in #1128
• Fixed PATH in the Pixi Docker template so commands resolve in OCI-to-SIF converted images by @munishchouhan in #1131

General​

• Fixed blob transfer jobs reporting success after uploading a 0-byte object by surfacing transfer errors when caching blobs (COMP-2142) by @stefanoboriero in #1100

Full changelog: https://github.com/seqeralabs/wave/compare/v1.37.0...v1.38.0