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Nextflow 26.02.0-edge

  • Add agent output mode (NXF_AGENT_MODE) [eae9f7d09]
  • Allow boolean params to implicitly default to false (#6764) [775a0fb87]
  • Ensure main script is first in the WorkflowRun lineage record (#6845) [ef01581d5]
  • Fix AgentLogObserver println clash with Groovy GDK method [c6314d7b5]
  • Fix AnsiLogObserver sticky messages duplicated when lines wrap (#6852) [4a06f705a]
  • Fix missing space before revision in launch info (#6834) [f30d782f5]
  • Fix ResourcesAggregator deadlock with virtual thread executor (#6840) [7ac4f3ea9]
  • Fix S3 delete throwing DirectoryNotEmptyException due to eventual consistency (#6833) [f3ac49754]
  • Fix S3 lookup unbounded pagination with double call (#6851) [a2e67eb99]
  • Fix vertical alignment in timeline report (#6794) [bbe0a27c9]
  • Handle Azure Batch ActiveJobAndScheduleQuotaReached with retry (#6874) [6e66aaa58]
  • Report actual GCP zone in Google Batch trace records (#6855) [465791294]
  • Sched core implementation alpha1 (#6242) [870c858af]
  • Treat LSF job status UNKWN as HOLD (#5756) [63aae8933]
  • Update default Azure Batch VM image to Ubuntu 24.04 (#6844) [b621fc7cb]
  • Use explicit memory units for LSF executor (#5217) [a369d6f33]

https://github.com/nextflow-io/nextflow/releases/tag/v26.02.0-edge

Nextflow 26.01.1-edge

Feature updates and improvements​

General​

  • Added OSC 8 hyperlinks to task hashes in progress output by @bentsherman in #6799
  • Improved documentation of workflow outputs by @bentsherman in #6822

Dependencies​

  • Bumped ch.qos.logback@1.5.26 to fix false version mismatch warning in shadow JAR by @pditommaso in 0b97f4a
  • Bumped ch.qos.logback@1.5.25 (CVE-2026-1225) by @pditommaso in 97dec3a
  • Bumped com.gradleup.shadow@9.3.1 (CVE-2025-68161) by @pditommaso in d31e6ed

Bug fixes​

Language features​

  • Fixed listDirectory() to follow symbolic links by @bentsherman in #6821

General​

  • Fixed JGit resources not being closed in CLI commands by @pditommaso in #6795

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.1-edge

Seqera Enterprise v25.3.3

Feature updates and improvements​

Studios​

  • (Public preview) Added SSH connectivity to Studios which enables direct connection to running Studio sessions using standard SSH clients, supporting VS Code Remote SSH and terminal access. See Studios SSH configuration for more information.

Pipelines​

  • Added custom schema support to pipeline versions.
  • Added edit launch pipeline.
  • Enabled custom schema retrieval for pipeline versions.

See Pipeline versioning for more information.

Access Control​

  • Removed participants on workspace deletion.
  • Improved error message when deleting custom roles.
  • Added pagination to roles list page.
  • Added the ability to view an effective permissions summary for any user/workspace combination in the UI or via API.
  • Added the ability to reset a custom role's permissions to match any predefined role (Admin, Maintain, Launch, Connect, View).

Custom roles quota enforcement​

The maxCustomRolesPerOrg quota is now enforced on custom role creation. Organizations at or near their quota limit will be unable to create additional custom roles. Review your organization's custom role usage if you need to create additional roles. Contact support to adjust your quotas if needed.

General​

  • Restored custom navigation menu support in user dropdown.
  • Updated styles for container responsiveness and padding adjustments and footer.
  • Added only current page in task pagination.
  • Added storage for SSH public keys for use in Studios.

Bug fixes​

  • Cleared parameters when changing between pipeline with and without parameters.
  • Fixed correctly updated versions list when version is published.
  • Prevented re-assignations of pipeline.launch when working with versions.
  • Updated schema when schemaName field value changes.
  • Prevented adding empty parameters when reseting parameters form with defaults after config profile change.

Upgrade steps​

This release maintains backward compatibility with version 25.2.x.

note
  • Make a backup of your Platform database prior to upgrade.
  • If you are upgrading from a version prior to 25.1, complete all intermediate major version upgrades before upgrading to 25.3.
  • Ensure that no pipelines or Studio sessions are in a running state during this upgrade as active run data and analysis may be lost.

See Upgrade deployment for installation guidance.

Nextflow 25.10.4

Feature updates and improvements​

Language features​

  • Removed unnecessary runtime checks with strict syntax by @bentsherman in #6539

AWS Batch​

  • Added isCompleted check in getNumSpotInterruptions by @munishchouhan in #6806

Dependencies​

  • Bumped nf-amazon@3.4.4 by @pditommaso
  • Bumped nf-google@1.23.5 by @pditommaso
  • Bumped nf-tower@1.17.5 by @pditommaso

Bug fixes​

Language features​

  • Fixed false error with optional param by @bentsherman in #6811
  • Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
  • Fixed false error in v2 parser when including config file from http url by @bentsherman in #6753

General​

  • Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.4

Nextflow 26.01.0-edge

Feature updates and improvements​

Language features​

  • Allowed collection-type params to be loaded from files by @bentsherman in #6675
  • Enabled v2 syntax parser by default by @bentsherman in #6643
  • Improved config syntax errors by @bentsherman in #6721
  • Improved error message for invalid config statements by @bentsherman in #6804
  • Improved error messages for workflow outputs by @bentsherman in #6785
  • Moved task hashing logic to TaskHasher class by @bentsherman in #6572

AWS Batch​

  • Added aws.batch.forceGlacierTransfer config option by @munishchouhan in #6700

Google Batch​

  • Refactored GoogleBatchTaskHandler.newSubmitRequest for reduced complexity by @pditommaso in #6687

Kubernetes​

  • Added time-based caching for K8sConfig.getClient() by @munishchouhan in #6742

Configuration​

  • Supported multiple config option types in config spec by @bentsherman in #6720

General​

  • Added accelerator request to trace record by @munishchouhan in #6703
  • Added CloudCacheConfig to register cloudcache config options by @pditommaso in #6774
  • Added markdown output mode to lint command by @ewels in #6715
  • Added missing provider credentials when updating the bare repo in multi-revision assets by @jorgee in #6698
  • Added warning stats to lint summary output by @ewels in #6714
  • Added workflow manifest metadata to execution report by @bentsherman in #6689
  • Detected conda explicit files by content instead of extension by @bentsherman in #6713
  • Excluded nf-test.config from lint by default by @ewels in #6716
  • Used conda-forge and bioconda channels by default by @Midnighter in #5423

Dependencies​

  • Bumped Groovy to 4.0.30 by @pditommaso in #6747
  • Bumped Spock 2.4 by @pditommaso in #6681

Bug fixes​

Language features​

  • Fixed caching of task ext properties with the strict parser by @bentsherman in #6696
  • Fixed compiler error in v2 parser with enums by @bentsherman in #6781
  • Fixed different task hash with v2 parser by @bentsherman in #6789
  • Fixed false error in v2 parser when including config file from http url by @bentsherman in #6753
  • Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
  • Fixed false error with optional param by @bentsherman in #6811
  • Fixed issue with topic file emissions in typed processes by @bentsherman in #6688
  • Fixed params inclusion across modules in v2 parser by @bentsherman in #6766
  • Fixed resolution of nested Groovy class in v2 parser by @bentsherman in #6744
  • Fixed type inference in v2 ConfigDsl by @bentsherman in #6800

AWS Batch​

  • Fixed AWS Batch spot instance detection by @munishchouhan in #6722
  • Fixed isCompleted check in getNumSpotInterruptions by @munishchouhan in #6805

S3​

  • Fixed error when checking whether an S3 bucket exists by @jorgee in #6706

Kubernetes​

  • Fixed K8s job fallback to not return incorrect zero exit code by @munishchouhan in #6746

General​

  • Fixed fetching new remote branch in multi-revision mode by @jorgee in #6733
  • Fixed lint error formatting for errors at end of line by @ewels in #6717
  • Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787
  • Fixed nextflow inspect not applying container settings from config by @adam-novak in #6736
  • Fixed spurious WARN when workflow fails before onFlowBegin by @pditommaso in #6816

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.0-edge

Fusion v2.4.20

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.20-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.20-arm64.json'.

Feature updates and improvements​

Fusion Snapshots​

  • Added support for Fusion Snapshots in Google Batch. See Fusion Snapshots for more information.
  • Added cleanup for dump folder following Spot termination to prevent unwanted storage costs.

Logging​

  • Better log readability: Added [seqera-fusion] prefix to console logs for easier identification in mixed output environments.
  • Improved error messages: Added more context and clearer wording to cloud provider errors, including better messages for archived/cold storage objects.

Troubleshooting​

Bug fixes​

AWS​

  • Fixed misleading "file not found" errors: Changed permission errors (403 Forbidden) from cloud providers to display as "Permission denied" instead of incorrectly showing "No such file or directory" (#1068).

General​

  • Cloud errors now log properly: Fixed an issue where cloud service errors were silently treated as simple "file not found" cases instead of logging and reporting properly (#1077).

Upgrade notes​

  • Drop-in replacement for v2.4.x. No configuration changes required.

Fusion v2.5.9

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.9-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.9-arm64.json'.

Feature updates and improvements​

Fusion Snapshots​

  • Added support for Fusion Snapshots in Google Batch. See Fusion Snapshots for more information.
  • Added cleanup for dump folder following Spot termination to prevent unwanted storage costs.

Logging​

  • Branded console logs: Added [seqera-fusion] prefix to all console logs for better identification in mixed output environments.
  • Real-time terminal output: Changed command output to display immediately in the terminal instead of buffering, improving visibility during execution.
  • Clearer error messages: Improved error messaging for non-recoverable I/O errors and archived objects.

Troubleshooting​

Bug fixes​

AWS​

  • Fixed AWS S3 Forbidden errors not mapping properly to permission denied.

General​

  • Fixed cloud storage errors not logging properly in certain scenarios.

Upgrade notes​

  • Drop-in replacement for v2.5.x. No configuration changes required.

Nextflow 25.10.3

Feature updates and improvements​

  • Added Channel::mix(Value...) by @bentsherman in a2bb57158
  • Added spot interruption tracking to trace records by @munishchouhan in #6606

Bug fixes​

  • Fixed nextflow inspect not applying container settings from config by @ewels in #6736
  • Fixed false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fixed issue with topic file emissions in typed processes by @stekaz in #6688
  • Fixed optional param in params block by @bentsherman in #6657
  • Fixed validation of numeric types in params block by @bentsherman in #6656
  • Fixed ignore multi-revision folder in list command by @jorgee in #6678

Dependencies​

  • Bumped nf-amazon@3.4.3
  • Bumped nf-google@1.23.4
  • Bumped nf-tower@1.17.4

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.3