Migrating to 24.10

Nextflow 24.10 was released on October 27, 2024.

New features

Language server

The Nextflow language server implements the Language Server Protocol (LSP) for Nextflow scripts and config files. It can be integrated with any editor that functions as an LSP client, and is used by the official Nextflow VS Code extension. See VS Code integration for details.

The language server parses scripts and config files according to the Nextflow language specification, which is more strict than the Nextflow CLI. See Preparing for strict syntax for details.

Workflow outputs (second preview)

The second preview of workflow outputs introduces the following breaking changes from the previous version:

  • The publish: section within processes has been removed. Channels should now be published only from workflows, ideally the entry workflow.

  • The directory output directive has been replaced with the outputDir config option and -output-dir command line option, which defaults to results. Other directives, such as mode, have been replaced with config options under workflow.output.*.

    In other words, only target blocks can be specified in the output block, but target blocks can still specify directives such as mode.

  • Target names cannot begin or end with a slash (/).

See Workflow outputs to learn more about the workflow output definition.

Enhancements

Azure Managed Identities

Nextflow now supports managed identities for the Azure Batch executor. See Managed identities for details.

Task previous execution trace

The task variable in the process definition has two new proprties, task.previousTrace and task.previousException, which allows a task to access the runtime metadata of the previous attempt. See Dynamic task resources with previous execution trace for details.

Breaking changes

  • The all release of Nextflow has been replaced with the dist release, which includes fewer core plugins by default and supports third-party plugins. See Standalone distribution for details.

  • The nf-ga4gh plugin has been moved into its own repository, nextflow-io/nf-ga4gh. To continue using the TES executor, you must explicitly declare the nf-ga4gh plugin in your Nextflow configuration. Refer to the plugin repository for documentation and updates on GA4GH integrations.

  • The HyperQueue executor now requires HyperQueue 0.17.0 or later.

  • The use of Grape dependencies with the @Grab annotation is no longer supported. Code that requires third-party libraries should be migrated to a plugin.

  • Automatic spot retries for AWS Batch and Google Batch have been disabled by default. See Spot Instance failures and retries for details.

Deprecations

  • The use of addParams and params clauses in include declarations is deprecated. See Module parameters for details.

Miscellanous

  • New config option: aws.client.requesterPays

  • New config option: google.batch.autoRetryExitCodes

  • New config option: google.batch.bootDiskImage

  • New config option: manifest.contributors

  • New config option: wave.mirror

  • New config option: wave.scan.mode

  • New config option: wave.scan.allowedLevels

  • New config option: workflow.failOnIgnore

  • Rename nextflow.publish.retryPolicy config scope to workflow.output.retryPolicy