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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

Fusion v2.5.15

Fusion v2.5.15 adds the per-task metrics file and fixes directory renames and snapshot resume for relaunched tasks.

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.15-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.15-arm64.json'.

Feature updates and improvements​

Metrics​

  • Added the per-task metrics file .fusion/metrics.jsonl.gz, written to each task work directory every 10 seconds. It is on by default. Set FUSION_METRICS_ENABLED=false to turn it off. See Fusion task metrics.

Bug fixes​

General​

  • Fixed renamed directories losing nested files and symbolic links that were not yet uploaded.
  • Fixed renames of directories with many new files failing with Connection timed out.
  • Fixed a deleted file reappearing after it was deleted, recreated, and deleted again.

Fusion Snapshots​

  • Fixed relaunched tasks not finding their snapshot. This regression affected v2.5.13 and v2.5.14.

Dependencies​

  • Removed the unused FUSION_MIN_FREE, FUSION_CACHE_SIZE, FUSION_CACHE_SOFT_LIMIT, FUSION_CACHE_HARD_LIMIT, FUSION_CLOSE_FILES, and FUSION_READ_AHEAD variables.
  • Updated the Go toolchain to 1.25.14.
  • Updated CI, build pipeline, and dependencies.

Upgrade notes​

  • Drop-in replacement for v2.5.14. No configuration changes required.
  • The removed variables already had no effect. You can delete them from your configuration.

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.

Nextflow 26.10.0

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

Wave v1.40.1

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

Nextflow 26.04.7

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