Breaking changes​

A Fusion version selected in the launch form or saved on a pipeline no longer takes effect on its own. Runs use the Fusion version from the Nextflow launcher container unless the Fusion version override is enabled on the compute environment.

Feature updates and improvements​

Co-Scientist​

• Moved the current page out of the status bar and onto a Context chip in the composer, where it stays visible after a page screenshot is skipped or dismissed.
• Added arrow-key navigation into and out of a category in the @ mention menu.
• Changed Esc at the top level of the @ mention menu to close the panel instead of reopening it.

Agents​

• Added the bound GitHub App credential to an agent's Details tab.
• Added a message to the Service account picker on the agent form when the workspace has no service account.

Actions​

• Added a link from an action's Target card to the agent it runs.
• Added a message to the Agent picker on the action form when the workspace has no agent.

Bug fixes​

Compute environments​

• Fixed cancelling a run on Google Batch failing and leaving its task jobs running.
• Fixed runs on EC2 instance types without live console output being marked unknown and dropped from monitoring.

Pipelines​

• Fixed resuming a run disabling every compute environment when the environment's work directory ends in a slash.

Feature updates and improvements​

Language features​

• Addressed limitations in agent inputs and outputs by @bentsherman in #7750
• Checked typed output names and allowed single named outputs by @bentsherman in #7769
• Deprecated the process when section in favor of the process.when config setting by @bentsherman in #7746
• Inferred the element type of empty channels, lists, and maps from first use by @bentsherman in #7774
• Made exit() graceful and reported an error for return statements in the workflow body by @bentsherman in #7570

Configuration​

• Allowed run-level cpus and memory limits for grid executors by @raphaelbetschart in #7783

General​

• Added a deprecations page to the docs by @bentsherman in #7766
• Improved the error message for local paths in module commands by @bentsherman in #7779

Bug fixes​

Language features​

• Fixed nullable workflow emits wrapping null in a dataflow value by @bentsherman in #7760
• Fixed static typing issues found while migrating a pipeline by @bentsherman in #7722

Google Batch​

• Fixed Google Batch array status polling for arrays of 500+ tasks by @robsyme in #7767
• Fixed Google Batch array task status cache never matching by @robsyme in #7778
• Fixed Google Batch task listing not retrying errors after the first page by @robsyme in #7768
• Fixed retried Google Batch job submissions failing with ALREADY_EXISTS by @pditommaso in #7762

General​

• Fixed interactive CLI prompts when stdin is not a terminal by @pditommaso in #7641
• Fixed the main thread exiting before the flow completes when aborted on another thread by @stefanoboriero in #7781
• Fixed IllegalThreadStateException aborting the session on task timeout by @Mohit-Ak in #7571
• Fixed invalid JSON sent to Seqera Platform when a value fails to serialize in TowerJsonGenerator by @pinin4fjords in #7772

Dependencies​

• Bumped nf-agent@0.2.0
• Bumped nf-agent-pi@0.6.0
• Bumped nf-amazon@3.12.0
• Bumped nf-google@1.29.0
• Bumped nf-tower@1.32.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.0

Feature updates and improvements​

General​

• Migrated wave-cli into the Wave repository by @pditommaso in #1156
• Enabled Renovate for all dependencies by @arnaualcazar in #1155

Dependencies​

• Pinned @typespec/openapi to 1.16.0 by @pditommaso in #1173
• Bumped Micronaut to 4.10.20 by @pditommaso in #1171
• Bumped condasplit frontend Go dependencies to fix vulnerabilities by @pditommaso in #1172
• Updated GitHub Actions by @seqeralabs-renovate[bot] in #1168
• Updated cr.seqera.io/public/nf-jdk Docker tag to v25.0.4 by @seqeralabs-renovate[bot] in #1166
• Bumped logback to 1.5.34 by @pditommaso in #1174
• Overrode vulnerable transitive JVM dependencies by @pditommaso in #1175
• Bumped Micronaut to 4.10.21 by @pditommaso in #1176

Full changelog: https://github.com/seqeralabs/wave/compare/v1.40.0...v1.40.1

Bug fixes​

Language features​

• Fixed error checking in workflow emits by @bentsherman in #7058
• Fixed the formatter dropping the main: label when onComplete: or onError: is present by @ewels in #7346

Configuration​

• Fixed config rendering of nested closures by @bentsherman in #7375

S3​

• Fixed S3 directory upload skipping symbolic links by @jorgee in #7515

Dependencies​

• Bumped vulnerable dependencies to patched releases by @jorgee in #7598
• Bumped nf-amazon@3.9.3
• Bumped nf-azure@1.22.7
• Bumped nf-codecommit@0.5.4
• Bumped nf-google@1.27.4
• Bumped nf-k8s@1.5.5
• Bumped nf-seqera@0.21.2
• Bumped nf-tower@1.28.3

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.7

Feature updates and improvements​

Language features​

• Added pipeline composition by @bentsherman in #7213
• Allowed any return type for a closure with a boolean signature by @bentsherman in #7688
• Added type checking for the type arguments of call arguments by @bentsherman in #7728
• Improved lint errors for common gotchas by @bentsherman in #7742
• Moved v1 process output resolution to TaskOutputResolverV1 by @bentsherman in #7036
• Published workflow outputs with FilePublisher by @bentsherman in #7745
• Added recognition of Record::subMap() in the type checker by @bentsherman in #7743
• Added an error for a closure or function that returns no value by @bentsherman in #7714
• Added an error for a missing return statement in a closure or function by @bentsherman in #7738
• Changed invalid script definitions to report the real syntax error by @bentsherman in #7675
• Added a type error for record field assignment by @bentsherman in #7718
• Skipped argument checks for plugin functions in typed scripts by @bentsherman in #7726
• Added support for a map of source-to-target pairs in the output path directive by @bentsherman in #7646
• Changed unnamed typed process outputs to use the inferred type by @pditommaso in #7757
• Added runtime validation of record fields for process record inputs by @bentsherman in #7692

Configuration​

• Added the seqera.executor.machineRequirement.onDemandCostRatio option by @pditommaso in #7710

Wave​

• Added conda/micromamba:v2-fast and conda/pixi:v1-fast to the wave.build.template docs by @pditommaso in #7727

General​

• Centralized shared dependency versions in gradle.properties by @pditommaso in #7704
• Made HashBuilder.isAssetFile public by @jorgee in #7723
• Changed CSV output to quote values only when required by @xHaMMaDy in #7377
• Changed lineage to record only tasks that completed by @jorgee in #7664
• Replaced LockManager with Guava Striped locks by @pditommaso in #7736
• Changed sched multi-attempt tasks to report the final attempt's start time by @pditommaso in #7755
• Changed the console log to go to stderr when ANSI logging is disabled by @bentsherman in #7741
• Added CI validation of agent examples against a staged runner image by @pditommaso in #7761

Bug fixes​

Language features​

• Fixed formatting of directives with a list argument by @bentsherman in #7679
• Fixed lineage path references for typed processes by @jorgee in #7713
• Fixed an NPE when all publish statements in a workflow output are no-ops by @bentsherman in #7674
• Fixed an NPE when publishing an external file with a publish statement by @bentsherman in #7721
• Fixed record cast of non-local Path values by @bentsherman in #7684
• Fixed serialization of dataflow params by @pinin4fjords in #7759
• Fixed the params block breaking piped operators in the entry workflow by @bentsherman in #7405

Plugins​

• Fixed plugin functions that return or take a channel by @bentsherman in #7715

General​

• Fixed a grep broken pipe error when reading the CPU model in the trace script by @bentsherman in #7672
• Fixed stale ANSI log lines when COLUMNS does not match the terminal width by @pditommaso in #7705
• Fixed the launcher Java version cache and md5 fallback by @ewels in #7695
• Fixed LsfExecutor.parseJobId() swallowing submit failures by @Arthur031221 in #7730
• Fixed the validate.sh image override with a relative results directory and Wave images by @pditommaso in #7763

Dependencies​

• Bumped Jackson to 2.21.7 and 2.18.11 to fix security advisories by @jorgee in #7732
• Bumped nf-agent-pi to 0.5.4 with pi-coding-agent 1.0.2 so the catalog includes GPT-6 Luna by @edmundmiller in #7748
• Bumped pi-coding-agent to 0.86.1 to fix undici advisories by @jorgee in #7733
• Bumped sched-client to 0.100.0 in nf-seqera by @pditommaso in fe446ce6d
• Bumped slf4j to 2.0.20 by @pditommaso in #7703
• Bumped nf-agent@0.1.2
• Bumped nf-agent-pi@0.5.4
• Bumped nf-azure@1.24.1
• Bumped nf-google@1.28.2
• Bumped nf-seqera@0.26.0
• Bumped nf-tower@1.31.0
• Bumped nf-wave@1.22.2

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.09.2-edge

Feature updates and improvements​

Co-Scientist​

• Replaced the Recent shortcut in the @ mention menu with a Search context field, per-category browsing, paginated results, and status badges.

Compute environments​

• Added Use private address to Azure Batch Forge compute environments, for pool nodes without public IP addresses.
• Added the instance ID and failing command to setup script warnings in the run execution log.

Studios​

• Added a link from a Studio's details page to its compute environment.

Service accounts​

• Added service accounts: non-human identities that belong to an organization and that an agent can run as. Organization owners add, view, edit, and delete them from the new Service accounts tab under Access control.
• Added workspace roles for service accounts.
• Added organization membership rules for service accounts. Each service account counts toward the organization's member limit.
• Marked service accounts in the admin panel. The users list and the Members of organization and Workspace participants tabs show a service account badge and a distinct avatar, and the organization role column reads Service account.

General​

• Redesigned the organization, workspace, and user profile settings pages.

Bug fixes​

Co-Scientist - projects​

• Fixed the project Datasets tab showing unusable dataset actions to Launch users and non-functional buttons in empty projects.
• Fixed relaunching a run from a project's Runs tab returning to the workspace instead of the project.

Pipelines​

• Fixed Launch users being unable to resume runs of pipelines with Pull latest enabled.
• Fixed Azure data repositories selected as a run output directory producing an invalid path.
• Fixed a Fusion version selected in the launch form ignoring the compute environment's Fusion snapshots setting. A selected version with no Fusion snapshots build now fails the launch with an error.

Compute environments​

• Fixed AWS compute environments reporting an unexpected error instead of an access denial when credentials cannot reach the work directory bucket.

Credentials​

• Fixed Bitbucket Server credentials with an access token and no password being rejected when adding a pipeline or opening its launch form.

Data Explorer​

• Fixed the IGV preview losing its reference annotation track, chromosome ideogram, and gene name search.

Data lineage​

• Fixed selecting a task in global search results opening the run's Tasks tab instead of the task.

Secrets​

• Fixed pipeline secrets with underscores in their names being wrongly rejected as duplicates.

General​

• Fixed muted text using the light theme color in the dark theme.
• Fixed muted and raised surfaces being indistinguishable in the dark theme.
• Fixed pipeline and compute environment addresses in the public 12.0.0.0/8 and 172.32.0.0-172.37.255.255 ranges being rejected as private.
• Fixed screen readers not announcing a field's label together with its value.

Seqera Platform Enterprise 26.2 adds event-driven Actions, triggered by bucket events, schedules, and pipeline run events. It also adds Co-Scientist agents that run as service accounts, a Projects view, a system-wide Nextflow version selector, and pre-flight validation for credentials and compute environments. Other additions are global search backed by the data lineage query language, customer-managed KMS encryption for pipeline secrets, and route-aware OpenTelemetry tracing. For identity and access management, 26.2 adds OIDC audience enforcement, RFC 8693 token exchange, refresh-token rotation, and more SCIM auditing.

Highlights​

• You can launch a pipeline with a specific Nextflow version, chosen from a system-wide catalog of nf-launcher images. Each compute environment type sets a minimum version. See Compute environments.
• Platform validates credentials and compute environments before launch, on a schedule, and on demand. Broken credentials surface before a run fails. This is enabled by default. See Upgrade notes.
• Actions can be triggered by a bucket event, a schedule, or a pipeline run event, can start an agent instead of a pipeline, and record a trigger history. The three triggers are enabled by default in every workspace.
• Global search, backed by the data lineage query language, searches across workspaces. It is on by default. To turn it off, set TOWER_GLOBAL_SEARCH_ENABLED to false.
• You can encrypt pipeline secrets with a customer-managed AWS Key Management Service (KMS) key, set with TOWER_AWS_SECRETS_KMS_KEY_ID.
• Enterprise deployments now send aggregate entity telemetry with the license check. This is enabled by default. See Upgrade notes.
• Co-Scientist chat is available to every organization in the installation. It is enabled by default once the Co-Scientist agent backend is configured. See Upgrade notes.
• You can configure reusable AI agents per workspace and start one from a run with Trigger agent. Each agent acts as its bound service account. Agents are enabled by default once the Co-Scientist agent backend is configured. See Upgrade notes.
• A Projects view groups a workspace's pipelines, datasets, and runs by project, and launches from a project use an essentials-only launch form. This is enabled by default in every organization workspace. See Upgrade notes.
• The standalone Co-Scientist web interface (provided by the portal-web chart) is removed. Co-Scientist is now part of Seqera Platform. See Upgrade notes.
• A component compatibility catalog records which Nextflow, Fusion, and nf-launcher artifacts work with this Platform version, with deployment-local overrides for private registries. This is enabled by default. See Upgrade notes.
• Platform can stamp the aud claim on the OIDC access tokens it issues and enforce it. Enforcement is off by default and only logs mismatches. See Upgrade notes.
• Studios support private sessions restricted to an allow-list of users, per-user favorites, and a configurable automated stop grace period.
• Route-aware OpenTelemetry tracing is available through the standard OTEL_* environment variables.
• Studios gain a Logs tab that streams a session's process log directly from the compute environment. Logs survive an ungraceful shutdown.
• The compute environment, credentials, and Actions lists are redesigned as row-card tables with attribute chips, grouping, and search.
• From 26.2, Seqera publishes one frontend container image, platform/frontend:<tag>, which runs in unprivileged mode. The -unprivileged tag alias and the -root variant, which ran as the root user, are gone. See Upgrade notes.
• Platform writes audit events only to the v2 schema. This is a breaking change for direct database consumers and ETL jobs that read the v1 tw_audit_log table. Update them to the v2 schema before you upgrade. See Upgrade notes.

Feature updates and improvements​

Container building​

• Added the conda/micromamba:v3 template with layered Conda builds by @pditommaso in #1146
• Renamed the conda/micromamba:v3 template to conda/micromamba:v2-fast by @pditommaso in #1151

Singularity​

• Added multi-architecture Singularity (SIF) build support by @pditommaso in #1140

General​

• Documented multi-platform container builds by @munishchouhan in #1137

Dependencies​

• Upgraded Micronaut platform to 4.10.19 (COMP-2257) by @cristianrcv in #1142
• Upgraded bouncycastle to 1.85 (COMP-2551) by @cristianrcv in #1141
• Upgraded typespec to 1.16.0 (COMP-2378) by @cristianrcv in #1143
• Upgraded lib-pairing to 1.1.1 to accept large pairing messages by @arnaualcazar in #1144
• Updated aws-actions/configure-aws-credentials action to v6.3.0 by @seqeralabs-renovate[bot] in #1139
• Updated anthropics/claude-code-action action to v1.0.231 by @seqeralabs-renovate[bot] in #1138

Full changelog: https://github.com/seqeralabs/wave/compare/v1.38.0...v1.39.0

Fusion v2.6.10 fixes a regression introduced in v2.6.9 that failed successful snapshot tasks with exit code 174. If you run Fusion Snapshots on v2.6.9, upgrade.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.10-amd64.json'
}

Bug fixes​

Fusion Snapshots​

• Fixed successful snapshot tasks failing with exit code 174 when the task deleted a temporary file it still had open.

Upgrade notes​

• Drop-in replacement for v2.6.9. No configuration changes required.
• If you pinned snapshot tasks to v2.6.8 to avoid the exit code 174 failures, you can unpin them.

Fusion v2.6.9 fixes three ways a healthy task could be lost in NFS service mode or on EC2: failed output uploads reported as success, a short EC2 instance metadata outage blocking S3 access, and remote I/O errors on a task relaunched from a clean start.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.9-amd64.json'
}

Bug fixes​

NFS service mode​

• Fixed a task exiting with 0 when the final upload of its work directory failed. Fusion now retries the upload for about five minutes, then exits with 174. See Fusion exit codes.
• Fixed a Remote I/O error when a task relaunched from a clean start recreated a path the clean had removed.

AWS​

• Fixed a short gap in the EC2 instance metadata service leaving Fusion with anonymous S3 access for the rest of the task. If the work directory is still unreachable, Fusion exits with 173, which Intelligent Compute relocates to another host.

Dependencies​

• Updated dependencies and CI.

Upgrade notes​

• Drop-in replacement for v2.6.8. No configuration changes required.
• In NFS service mode, a task whose command succeeded but whose final work directory upload failed now exits with 174 instead of 0. A task whose command failed keeps its original exit code.
• On EC2, a host with no instance profile keeps using anonymous S3 access. If a host has an instance profile but no reachable instance metadata service and should use anonymous access, set AWS_EC2_METADATA_DISABLED=true.