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Nextflow 26.10.3

Rotate Bitbucket Cloud API tokens

This release keeps Bitbucket Cloud API tokens out of git clone URLs and logs. If you authenticated with a Bitbucket API token on 25.07.0-edge through 26.10.2, rotate the token. It may have been written to console output, .nextflow.log files, and the .git/config of cloned pipelines. See #7868.

Bug fixes​

Language features​

  • Applied Harshil alignment to trailing comments, not annotations by @bentsherman in #7832
  • Fixed cascading type errors from inconsistently typed expressions by @bentsherman in #7851
  • Fixed hang in preview mode with workflow outputs by @bentsherman in #7838
  • Fixed onError section in entry workflow by @bentsherman in #7831
  • Fixed stdlib typos by @bentsherman in #7863
  • Fixed type checking of function calls that omit default params by @bentsherman in #7860
  • Fixed type of task.label in language definitions by @bentsherman in #7857

Configuration​

  • Fixed unrecognized config warnings for nextflow.retryPolicy options by @pditommaso in #7843

General​

  • Escaped control characters in task metadata and job names by @arnaualcazar in #7764
  • Removed the Bitbucket API token from git clone URLs and logs by @bentsherman in #7870

Dependencies​

  • Updated Grengine to 3.1.2 (group ID and package ch.grengine) by @alainstalder in #7842

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.3

Seqera Cloud v27.1.0_cycle77

Breaking changes​

Google credentials now accept only service account keys. Creating or updating a credential with a key of another type, a non-Google token URI, or a universe domain other than googleapis.com fails, and a stored credential that fails the same check becomes invalid at its next validation. Workload Identity Federation credentials are unchanged.

Feature updates and improvements​

Compute environments​

  • Added Fusion version and Fusion snapshots settings to the compute environment, pipeline, and launch forms.

Studios​

  • Added a capacity check that blocks a Studio when its AWS Batch compute environment is full, and reports a session waiting for resources.

Agents​

  • Renamed the agent Pause and Resume actions to Disable and Enable.

Co-Scientist​

  • Changed a new conversation to bill the organization of the workspace it starts from, rather than one inferred from the page.

Datasets​

  • Moved the datasets table to the comfortable layout, with taller rows and more space in each cell.
  • Added a View hint to the runs link on a dataset row.

Pipelines​

  • Added Nextflow 26.10.0 to the version catalog.

Data Explorer​

  • Added a specific error for a bucket the selected credentials cannot access, in place of a generic failure.
  • Moved the Data Explorer list from row cards to a headed table in the comfortable layout. Hidden now sits next to a repository's name, beside Public.

Bug fixes​

Compute environments​

  • Fixed a Google Cloud head VM staying up when its first self-delete was refused. It now retries for up to an hour.
  • Fixed an Azure Cloud run that ends before Nextflow reports its start giving no diagnosis. The error now points to the head's launcher output.
  • Fixed AWS Forge leaving s3:AbortMultipartUpload out of the policy it writes for the work directory bucket, where a failed or canceled multipart upload left incomplete parts behind. Compute environments created before this release keep their existing policy.
  • Fixed a Studio on a Google Cloud compute environment failing to pull a private container image from Artifact Registry or Container Registry. The head VM now authenticates to the registry with its own identity.

Pipelines​

  • Fixed the launch form leaving nested run parameters empty when a config profile set them.
  • Fixed a long version name misaligning the columns of the Launchpad list.
  • Fixed editing a pipeline's Seqera Platform schema failing with an "already exists" error when the schema declares an $id.

Co-Scientist​

  • Fixed a conversation showing no feedback while its transcript loaded.

Agents​

  • Fixed a failed agents list showing the "No agents configured yet" empty state instead of an error.

Projects​

  • Fixed the project edit form omitting project pipelines that sorted past the first page.

Data Explorer​

  • Fixed the data picker offering Upload to users without permission to upload.

Credits​

  • Fixed storage and network usage not being priced, so it never drew from credit grants.

Monitoring and observability​

  • Fixed a run with no output directory showing a lineage message on its Outputs tab.
  • Fixed folders on a run's Outputs tab not expanding. The pipeline outputs list is now always a tree.

Studios​

  • Fixed long Studio names truncating in the Studios list while the name column still had room.

General​

  • Fixed form controls not repainting after a silent value update.
  • Fixed the Fusion throughput quota never applying at launch.

Wave v1.42.0

Feature updates and improvements​

General​

  • Moved job queues to lib-data-workqueue, fixed duplicate job processing, and drained the queues on shutdown by @pditommaso in #1201
  • Named the Wave image path in the self-install guides by @robsyme in #1179

Dependencies​

  • Updated postgres Docker tag to v16.15 by @seqeralabs-renovate[bot] in #1198
  • Updated npm minor and patch dependencies by @seqeralabs-renovate[bot] in #1197
  • Updated GitHub Actions by @seqeralabs-renovate[bot] in #1195

Full changelog: https://github.com/seqeralabs/wave/compare/v1.41.0...v1.42.0

Wave v1.41.0

Feature updates and improvements​

Container building​

  • Kept only the platform's Fusion snapshot layer in multi-arch images by @pditommaso in #1191
  • Dropped the other platform's layers from frozen multi-arch container files by @pditommaso in #1193

General​

  • Matched registry credentials by repository path by @cristianrcv in #1165
  • Disabled SSRF protection by default by @pditommaso in #1192
  • Published condasplit with the Wave release and checked that its default matches VERSION by @pditommaso in #1188

Dependencies​

  • Bumped condasplit to v2 and checked the VERSION bump on pull requests by @pditommaso in #1187
  • Overrode the vulnerable jackson on the Gradle plugins classpath by @pditommaso in #1194

Bug fixes​

Container building​

  • Stripped stray leading blank line from extracted Conda lock file by @pinin4fjords in #1082

New contributors​

  • @pinin4fjords made their first contribution in #1082

Full changelog: https://github.com/seqeralabs/wave/compare/v1.40.4...v1.41.0

Nextflow 26.10.1

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

Wave v1.40.3

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

Seqera Cloud v27.1.0_cycle76

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.