Changelog

Fixes and improvements in AI summaries:​

• AI summaries should now work with bioconda install multiqc without additional dependencies
• Supporting other LLM providers with a custom endpoint passed through the command line (docs)
• Option to anonymize sample names

Bug fixes​

A change in the nf-core tools template made config profile search in the pipeline launch form inconsistent in Platform as it's prepended by a ternary operator. This release introduces a fix that improves config profile name parsing.

Feature updates and improvements​

• Remove server from OpenAPI spec by @munishchouhan in https://github.com/seqeralabs/wave/pull/793
• Add container index support to inspect view by @pditommaso in https://github.com/seqeralabs/wave/pull/792

Full changelog: https://github.com/seqeralabs/wave/compare/v1.17.0...v1.17.1

Feature updates and improvements​

• Bump BuildKit to version 0.18.2 by @pditommaso in https://github.com/seqeralabs/wave/pull/787
• Normalize URL in conda package while using them to generate target image by @munishchouhan in https://github.com/seqeralabs/wave/pull/786
• Update docs by @munishchouhan in https://github.com/seqeralabs/wave/pull/790
• Render html from OpenAPI spec generated by typespec by @munishchouhan in https://github.com/seqeralabs/wave/pull/707

Full changelog: https://github.com/seqeralabs/wave/compare/v1.16.8...v1.17.0

Bugfix release to improve stability.

Bug fixes​

• Logs removed when removeLogs is false
• Unique IDs in file fragments
• Remove exit code on serveFusion

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.1-amd64.json'
}

Breaking changes​

• Restore errorStrategy and maxRetries default Nextflow config for AWS and GCP launches. Platform will not overwrite existing error strategy coded in the pipeline repository.
• If you want to automatically retry on task failures (e.g., from spot reclamations), you will now need to explicitly set errorStrategy and maxRetries.
• Automatic spot retries in AWS and GCP need to be actively enabled. Alternatively the generic failure is handled at the Nextflow level.

You can revert to the default setting used in Nextflow prior to 24.10 with the following configuration options:

aws.batch.maxSpotAttempts = 5
google.batch.maxSpotAttempts = 5

Set task.maxRetries to a non-zero value to restore Platform to prior behaviour.

How do I retry Spot failures while making them visible?

There is no mechanism in Nextflow to specifically report Spot retries. However you can set process.maxRetries = 5 to retry all failures (including Spot reclamations) a specified number of times before failure.

Feature updates and improvements​

• Data Studios:
  • Added data studio API endpoints to the OpenAPI spec.
• New dynamic page title for easy bookmarking.
• Free tier:
  • New organization types added to allow free tier users to monitor their usage and limits.
• Restore errorStrategy default Nextflow config for AWS and GCP launches. The Nextflow job now correctly terminates after pipeline completion.
• Improved error messaging when pipeline info can't be fetched indicates whether the issue is due to a missing resource, or failed authentication due to expired credentials.
• Azure jobs are now automatically terminated after all tasks are complete.
• Send only added/updated run parameters when launching a pipeline. This includes all defaults and parameters passed during the launch.
• Updated list of EC2 families with NVMe disks available.
• Upgrade to Angular 17
• Bump Nextflow launcher to 24.10.3

Bug fixes​

• Allow unsetting schemaName when editing a pipeline.
• Use preferred_username as fallback email field for OIDC login.
• Drop the last characters in job definition name, if longer than the prescribed limit.
• Compute environment creation form allows pre- and post-run scripts to be longer than the accepted value of 1024 characters.
• Prohibit duplicate Git credentials and tie-break on lastUpdated for existing duplicates. Going forward, preference is given to the credentials updated last in the situation when there are multiple candidates. Additionally a duplicate check is added when creating new credentials, to avoid new duplicate cases.
• Disable reset selection on data change in workflow list component.
• Take into account the alternative mainScript path.

Bug fixes​

• Solves an issue with Git URLs in Azure DevOps.
• Bumps Nextflow launcher to 24.10.4.

Feature updates and improvements​

• Add TraceContextFilter logging context propagation by @pditommaso in 396c10c2
• Improve proxy cache configuration by @pditommaso in 163e605f
• Improve logging pattern by @pditommaso in 0ab87164
• Improve request caching logic by @pditommaso in a95153be
• Bump MN to 4.7.4 by @pditommaso in 4ce2a139

Full changelog: https://github.com/seqeralabs/wave/compare/v1.16.7...v1.16.8

Fusion 2.5.0 significantly enhances performance and efficiency in file operations.

Fusion now handles small files more effectively and intelligently manages Nextflow task files by minimizing intermediate file uploads. A key improvement is the selective retention of only essential task output files upon completion, reducing storage overhead. Network optimization has been implemented to decrease bandwidth usage by consolidating upload operations. Additionally, the underlying architecture has undergone substantial refactoring to support the future integration of diverse remote storage solutions, setting the foundation for expanded storage capabilities.

Feature updates and improvements​

• Chunked async content management
• Nextflow-compatible pattern classifier
• Define a default exit code on Fusion-IO errors
• Object API refactoring
• Bump golang.org/x/crypto to 0.31.0
• Bump golang.org/x/net to 0.33.0

Bug fixes​

• AsyncStore move issues
• Log file deletion during spot instance reclamation
• Transient object persistence

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.0-amd64.json'
}