Feature updates and improvements​

Google Batch​

• Fetched Google Batch task status once per trace record by @bentsherman in #7807
• Retried INTERNAL errors from the Google Batch API by @bentsherman in #7805

Plugins​

• Loaded the config files in the plugin commands session by @pditommaso in #7815

General​

• Retried foreign file staging on connection reset by @pditommaso in #7799

Bug fixes​

Language features​

• Fixed file-handling bugs in native processes by @bentsherman in #7789
• Fixed workflow output path closure returning an empty map by @bentsherman in #7823
• Fixed workflow variables named published or owner by @pinin4fjords in #7814

Google Batch​

• Fixed Google Batch array job deleted when a single array task is killed by @pditommaso in #7808

Fusion​

• Skipped Fusion .fusion directories when publishing directories by @pditommaso in #7811

General​

• Fixed unit tests that depend on global state from other tests by @bentsherman in #7804

Dependencies​

• Bumped nf-amazon@3.12.1
• Bumped nf-azure@1.24.2
• Bumped nf-google@1.29.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.1

Feature updates and improvements​

Plugins​

• Built plugin commands config in the CLI by @pditommaso in #7834

Bug fixes​

Language features​

• Fixed formatter treating comment-like GString text as a comment by @bentsherman in #7828

Dependencies​

• Bumped nf-tower@1.32.1
• Bumped nf-wave@1.22.3

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.2

Feature updates and improvements​

General​

• Published multi-arch (amd64 and arm64) Wave image on release and preview by @pditommaso in #1180

Dependencies​

• Updated github.com/moby/go-archive module to v0.3.0 (security) by @seqeralabs-renovate[bot] in #1177
• Bumped lib-cache-tiered-redis to 1.1.1 by @pditommaso in #1182
• Bumped lib-pairing to 1.2.0 by @pditommaso in #1184

Bug fixes​

General​

• Fixed token watcher head-of-line blocking on slow Platform endpoints by @jordeu in #1181

Full changelog: https://github.com/seqeralabs/wave/compare/v1.40.2...v1.40.3

This release contains no changes beyond the version bump.

Full changelog: https://github.com/seqeralabs/wave/compare/v1.40.3...v1.40.4

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.