From 464ccb789fd662867e042a6ab9591154c5dae958 Mon Sep 17 00:00:00 2001 From: Ben Sherman Date: Wed, 22 Oct 2025 19:37:44 -0500 Subject: [PATCH 1/2] Finalize 25.10 migration guide Signed-off-by: Ben Sherman --- docs/migrations/25-10.md | 36 ++++++++++++++++++++++++++++++------ 1 file changed, 30 insertions(+), 6 deletions(-) diff --git a/docs/migrations/25-10.md b/docs/migrations/25-10.md index 383a430333..d013fe8603 100644 --- a/docs/migrations/25-10.md +++ b/docs/migrations/25-10.md @@ -1,12 +1,8 @@ (migrating-25-10-page)= -# Migrating to 25.10 (preview) +# Migrating to 25.10 -This page summarizes the upcoming changes in Nextflow 25.10, which will be released in October 2025. - -:::{note} -This page is a work in progress and will be updated as features are finalized. It should not be considered complete until the 25.10 release. -::: +[Nextflow 25.10](https://github.com/nextflow-io/nextflow/releases/tag/v25.10.0) was released on October 22, 2025. ## New features @@ -148,6 +144,23 @@ Nextflow supports Groovy-style type annotations using the ` ` syntax See {ref}`migrating-static-types` for details. +

Auth and Launch commands

+ +The Nextflow CLI has two new commands: `nextflow auth` and `nextflow launch`. These commands allow you to authenticate with Seqera Platform and launch pipelines from the command line, providing a more streamlined experience over the previous approach of `nextflow run` using the `-with-tower` option. + +```bash +# authenticate with Seqera Cloud +nextflow auth login + +# check authentication status +nextflow auth status + +# launch a pipeline in Seqera Platform +nextflow launch nextflow-io/hello +``` + +See {ref}`cli-auth` and {ref}`cli-launch` for details. + ## Enhancements

Nextflow plugin registry

@@ -226,6 +239,8 @@ This feature addresses previous inconsistencies in timestamp representations. ## Breaking changes +- The `google-lifesciences` executor is no longer supported, since the Google Cloud Life Sciences API is no longer available since July 2025. Use the `google-batch` executor instead. + - The AWS Java SDK used by Nextflow was upgraded from v1 to v2, which introduced some breaking changes to the `aws.client` config options. See {ref}`the guide ` for details. - The `nextflow.config.schema` package was renamed to `nextflow.config.spec`. Plugin developers that define custom {ref}`configuration scopes ` will need to update their imports accordingly. @@ -235,3 +250,12 @@ This feature addresses previous inconsistencies in timestamp representations. - The legacy type detection of CLI parameters is disabled when using the strict syntax (`NXF_SYNTAX_PARSER=v2`). {ref}`Legacy parameters ` in the strict syntax should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`. - The use of workflow handlers in the configuration file has been deprecated. You should define workflow handlers in the pipeline script or a plugin instead. See {ref}`config-workflow-handlers` for details. + +- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The {ref}`strict syntax ` now validates process selectors without producing false warnings. + +## Miscellaneous + +- New config option: `docker.registryOverride` +- New config options: `wave.build.compression.*` +- New executor: Fujitsu Technical Computing Suite (`tcs`) +- Support Java 25 From 36c526141675fac468b2347b707882ee86e9dfd2 Mon Sep 17 00:00:00 2001 From: Ben Sherman Date: Thu, 23 Oct 2025 05:55:12 -0500 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: Chris Hakkaart Signed-off-by: Ben Sherman --- docs/migrations/25-10.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/docs/migrations/25-10.md b/docs/migrations/25-10.md index d013fe8603..643266d26e 100644 --- a/docs/migrations/25-10.md +++ b/docs/migrations/25-10.md @@ -146,16 +146,19 @@ See {ref}`migrating-static-types` for details.

Auth and Launch commands

-The Nextflow CLI has two new commands: `nextflow auth` and `nextflow launch`. These commands allow you to authenticate with Seqera Platform and launch pipelines from the command line, providing a more streamlined experience over the previous approach of `nextflow run` using the `-with-tower` option. +The Nextflow CLI has two new commands: `nextflow auth` and `nextflow launch`. Together, they allow you to authenticate with Seqera Platform and launch pipelines from the command line. This approach streamlines the previous workflow of using `nextflow run` with the `-with-tower` option. ```bash -# authenticate with Seqera Cloud +# Authenticate with Seqera Cloud nextflow auth login -# check authentication status +# Check authentication status nextflow auth status -# launch a pipeline in Seqera Platform +# Configure Seqera Platform settings +nextflow auth config + +# Launch a pipeline in Seqera Platform nextflow launch nextflow-io/hello ``` @@ -239,7 +242,7 @@ This feature addresses previous inconsistencies in timestamp representations. ## Breaking changes -- The `google-lifesciences` executor is no longer supported, since the Google Cloud Life Sciences API is no longer available since July 2025. Use the `google-batch` executor instead. +- The `google-lifesciences` executor is no longer supported because the Google Cloud Life Sciences API was discontinued in July 2025. Use the `google-batch` executor instead. - The AWS Java SDK used by Nextflow was upgraded from v1 to v2, which introduced some breaking changes to the `aws.client` config options. See {ref}`the guide ` for details.