From 68eb6d91cc0e149d470053636abb84a0e79a6fdc Mon Sep 17 00:00:00 2001 From: Gavin Elder Date: Thu, 5 Feb 2026 16:37:46 +0000 Subject: [PATCH 1/3] chore: Update Changelog providing additional nextflow details --- changelog/seqera-enterprise/v25.1.md | 43 +++++++++++++++++------- changelog/seqera-enterprise/v25.2.md | 42 ++++++++++++++++++++--- changelog/seqera-enterprise/v25.3.1.md | 46 ++++++++++++++++++++++---- changelog/seqera-enterprise/v25.3.md | 28 +++++++++++----- 4 files changed, 127 insertions(+), 32 deletions(-) diff --git a/changelog/seqera-enterprise/v25.1.md b/changelog/seqera-enterprise/v25.1.md index 29d068982..716cdb774 100644 --- a/changelog/seqera-enterprise/v25.1.md +++ b/changelog/seqera-enterprise/v25.1.md @@ -38,9 +38,9 @@ Studios is Seqera's in-platform tool for secure, on-demand, interactive data ana ### Pipelines - You can upload custom icons when adding or updating a pipeline. If no user-uploaded icon is defined, Platform will retrieve and attach a pipeline icon in the following order of precedence: - 1. A valid `icon` key:value pair defined in the `manifest` object of the `nextflow.config` file. - 2. The GitHub organization avatar (if the repository is hosted on GitHub). - 3. If none of the above are defined, Platform auto-generates and attaches a pipeline icon. + 1. A valid `icon` key:value pair defined in the `manifest` object of the `nextflow.config` file. + 2. The GitHub organization avatar (if the repository is hosted on GitHub). + 3. If none of the above are defined, Platform auto-generates and attaches a pipeline icon. - Updated the pipeline name regular expression to allow pipeline names containing dots ('.'). - Improved error messaging when pipeline information can't be fetched indicates whether the issue is due to a missing resource, or failed authentication due to expired credentials. @@ -62,17 +62,12 @@ Studios is Seqera's in-platform tool for secure, on-demand, interactive data ana - Allow users to remove organization logos. - Dashboard page: Add a date filter. -### Infrastructure - -- Bumped nf-launcher default to version 25.10.5. -- Upgraded to Angular 18. - ## Bug fixes ### Studios - Fixed resource labels erroneously non-editable for the Maintain role when adding or starting a Studio session. -- Fixed searches for names containing special SQL wildcard characters (_, %). +- Fixed searches for names containing special SQL wildcard characters (\_, %). ### Credentials @@ -102,6 +97,30 @@ Studios is Seqera's in-platform tool for secure, on-demand, interactive data ana - Use `preferred_username` as fallback email field for OIDC login. - Fixed a problem with Entra and `javax.mail` transitive dependency. +## Nextflow + +### Nextflow upgraded to 24.10.5 + +Seqera Platform 25.1 includes Nextflow 24.10.5 (previously 24.10.4 from v24.2). + +According to the [24.10.0](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.0) through [24.10.5](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.5) release notes, this update includes improvements and bug fixes. Existing pipelines will continue to work. + +See the [Nextflow 24.10 migration guide](https://www.nextflow.io/docs/latest/migrations/24-10.html) for full details. + +**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.1/launch/advanced#pre-and-post-run-scripts): + +```bash +export NXF_VER=24.10.4 +``` + +### Nextflow launcher image + +If you host your nf-launcher container image on a private image registry, copy the [nf-launcher](https://public.cr.seqera.io/repo/platform/nf-launcher) image to your private registry. Then update your `tower.env` with the following environment variable: + +`TOWER_LAUNCH_CONTAINER=` + +If you're using AWS Batch, you will need to configure a custom job-definition and populate the `TOWER_LAUNCH_CONTAINER` with the job-definition name instead. + ## Breaking changes and warnings ### OIDC Secrets injection modifications @@ -168,9 +187,9 @@ Upgrading to version 25.1 requires backend downtime in order for the database mi 1. This version requires a database schema update. Make a backup of your Platform database prior to upgrade. 1. If you are upgrading from a version older than 23.4.1, update your installation to version [23.4.4](https://docs.seqera.io/changelog/seqera-enterprise/v23.4) first, before updating to 25.1 with the steps below. 1. For recommended Platform memory settings, add the following environment variable to your Platform configuration values (`tower.env`, `configmap.yml`, etc.): - ```bash - JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144 - ``` + ```bash + JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144 + ``` 1. See [Upgrade installation](https://docs.seqera.io/platform-enterprise/24.2/enterprise/upgrade) for installation upgrade guidance. :::info diff --git a/changelog/seqera-enterprise/v25.2.md b/changelog/seqera-enterprise/v25.2.md index aec9ff2af..9e8b81454 100644 --- a/changelog/seqera-enterprise/v25.2.md +++ b/changelog/seqera-enterprise/v25.2.md @@ -96,10 +96,6 @@ Single instance compute environments create a single compute instance to execute ### API - Added OpenAPI tags to endpoints. - -### Infrastructure - -- Bumped Nextflow launcher to 25.04.x. - Added indexes to improve performance on some potentially slow queries. ## Bug fixes @@ -138,6 +134,41 @@ Single instance compute environments create a single compute instance to execute - Updated navigation bar link to Dashboard instead of Launchpad. - Improved error message handling for requests that have `RequestOptions.responseType` explicitly specified. +## Nextflow + +### Nextflow upgraded to 25.04.3 + +Seqera Platform 25.2 includes Nextflow 25.04.3 (previously 24.10.4). + +According to the [25.04.0](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.0) through [25.04.3](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.3) release notes, this is a major update with new features and some breaking changes. However, existing pipelines will continue to work. New recommended syntax is now available: + +**New features:** + +- **Workflow params**: New `params` block for declaring pipeline parameters with type annotations (requires strict syntax) +- **Type annotations**: Support for type annotations on parameters, workflows, processes, and functions (requires strict syntax) +- **Simpler syntax**: Workflow handlers and dynamic directives no longer require closures with strict syntax enabled + +**Breaking changes:** + +- AWS Java SDK upgraded from v1 to v2 (affects `aws.client` config options) +- Package `nextflow.config.schema` renamed to `nextflow.config.spec` + +See the [Nextflow 25.04 migration guide](https://www.nextflow.io/docs/latest/migrations/25-04.html) for full details. + +**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.2/launch/advanced#pre-and-post-run-scripts): + +```bash +export NXF_VER=24.10.4 +``` + +### Nextflow launcher image + +If you host your nf-launcher container image on a private image registry, copy the [nf-launcher](https://public.cr.seqera.io/repo/platform/nf-launcher) image to your private registry. Then update your `tower.env` with the following environment variable: + +`TOWER_LAUNCH_CONTAINER=` + +If you're using AWS Batch, you will need to configure a custom job-definition and populate the `TOWER_LAUNCH_CONTAINER` with the job-definition name instead. + ## General warnings ### Removed `maxSpotattempts` setting from Platform @@ -153,9 +184,10 @@ See [Legacy Seqera container image registries](https://docs.seqera.io/platform-e ## Upgrade steps :::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 25.2. - Ensure that no pipelines are in a running state during this upgrade as active run data may be lost. -::: + ::: See [Upgrade deployment](https://docs.seqera.io/platform-enterprise/25.2/enterprise/upgrade) for installation guidance. diff --git a/changelog/seqera-enterprise/v25.3.1.md b/changelog/seqera-enterprise/v25.3.1.md index 47c2d8176..c5842e943 100644 --- a/changelog/seqera-enterprise/v25.3.1.md +++ b/changelog/seqera-enterprise/v25.3.1.md @@ -4,14 +4,48 @@ date: 2025-12-16 tags: [seqera enterprise] --- -## Feature updates and improvements - -### Infrastructure - -- Bumped Nextflow launcher to `25.10.2`. - ## Bug fixes ### Compute environments - Resolved an issue with long-running jobs and sts caching. + +## Nextflow + +### Nextflow upgraded to 25.10.2 + +Seqera Platform 25.3.1 includes Nextflow 25.10.2 (previously 25.04.8). + +According to the [25.10.0](https://github.com/nextflow-io/nextflow/releases/tag/v25.10.0), [25.10.1](https://github.com/nextflow-io/nextflow/releases/tag/v25.10.1), and [25.10.2](https://github.com/nextflow-io/nextflow/releases/tag/v25.10.2) release notes, there are breaking changes for AWS configurations and the deprecated Google Life Sciences executor. However, existing pipelines will continue to work. New recommended syntax is now available: + +**New features:** +- **Workflow params**: New `params` block for declaring pipeline parameters with type annotations (requires strict syntax) +- **Workflow outputs out of preview**: Workflow outputs are now production-ready (remove `nextflow.preview.output` flag if using) +- **Type annotations**: Support for type annotations on parameters, workflows, processes, and functions (requires strict syntax) +- **Auth and Launch commands**: New `nextflow auth` and `nextflow launch` commands for Seqera Platform integration + +**Enhancements:** +- Nextflow plugin registry for more efficient plugin downloads +- Simpler syntax for workflow handlers (`onComplete`, `onError` sections in workflows) +- Simpler syntax for dynamic directives (no closure required with strict syntax) +- Configurable date formatting via `NXF_DATE_FORMAT` environment variable + +**Breaking changes:** +- `google-lifesciences` executor removed (use `google-batch` instead) +- AWS Java SDK upgraded from v1 to v2 (affects `aws.client` config options) +- Package `nextflow.config.schema` renamed to `nextflow.config.spec` + +See the [Nextflow 25.10 migration guide](https://www.nextflow.io/docs/latest/migrations/25-10.html) for full details. + +**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.3/launch/advanced#pre-and-post-run-scripts): +```bash +export NXF_VER=25.04.8 +``` + +### Nextflow launcher image + +If you host your nf-launcher container image on a private image registry, copy the [nf-launcher](https://public.cr.seqera.io/repo/platform/nf-launcher) image to your private registry. Then update your `tower.env` with the following environment variable: + +`TOWER_LAUNCH_CONTAINER=` + +If you're using AWS Batch, you will need to configure a custom job-definition and populate the `TOWER_LAUNCH_CONTAINER` with the job-definition name instead. diff --git a/changelog/seqera-enterprise/v25.3.md b/changelog/seqera-enterprise/v25.3.md index 0b9234693..ee6c8c07d 100644 --- a/changelog/seqera-enterprise/v25.3.md +++ b/changelog/seqera-enterprise/v25.3.md @@ -53,17 +53,9 @@ Seqera Platform Enterprise version 25.3 introduces a series of new features and - Added `f2.6xlarge`, `f2.12xlarge`, `f2.48xlarge` instance types. - Extended Google Cloud config with selectable **Advanced options** - `machineType`, `image`, `armEnabled`. -### Nextflow launcher image - -If you host your nf-launcher container image on a private image registry, copy the [nf-launcher](https://quay.io/repository/seqeralabs/nf-launcher?tab=tags) image to your private registry. Then update your `tower.env` with the following environment variable: - -`TOWER_LAUNCH_CONTAINER=` - -If you're using AWS Batch, you will need to configure a custom job-definition and populate the `TOWER_LAUNCH_CONTAINER` with the job-definition name instead. ## General -- Bumped Nextflow launcher to `nf-launcher:j21-25.04.8`. - Replaced the top navigation with a sidebar in Platform. - Updated Platform behavior to redirect to first available sidenav item instead of hardcoded launchpad. - Added usage statistics to the Datasets API, allowing you to view the number of pipeline runs using each dataset and when it was last used. @@ -121,8 +113,26 @@ See the [Wave changelog](https://docs.seqera.io/changelog/tags/wave) for more de ## Nextflow -See the [Nextflow migration notes page](https://www.nextflow.io/docs/latest/migrations/index.html) for changelog details. +### Nextflow upgraded to 25.04.8 + +Seqera Platform 25.3 includes Nextflow 25.04.8 (previously 25.04.3 from v25.2). + +According to the [25.04.0](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.0) through [25.04.8](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.8) release notes, this update includes bug fixes and stability improvements. Existing pipelines will continue to work. +See the [Nextflow 25.04 migration guide](https://www.nextflow.io/docs/latest/migrations/25-04.html) for full details. + +**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/launch/advanced#pre-and-post-run-scripts): +```bash +export NXF_VER=25.04.x +``` + +### Nextflow launcher image + +If you host your nf-launcher container image on a private image registry, copy the [nf-launcher](https://public.cr.seqera.io/repo/platform/nf-launcher) image to your private registry. Then update your `tower.env` with the following environment variable: + +`TOWER_LAUNCH_CONTAINER=` + +If you're using AWS Batch, you will need to configure a custom job-definition and populate the `TOWER_LAUNCH_CONTAINER` with the job-definition name instead. ## MultiQC See the [MultiQC changelog](https://docs.seqera.io/changelog/tags/multiqc) for details. From 7955f647884d8d442f7897bd405fc37ef4c5fdf7 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Fri, 6 Feb 2026 21:18:02 +0200 Subject: [PATCH 2/3] Update v25.1.md Signed-off-by: Justine Geffen --- changelog/seqera-enterprise/v25.1.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/changelog/seqera-enterprise/v25.1.md b/changelog/seqera-enterprise/v25.1.md index c02791b82..5306a1b4a 100644 --- a/changelog/seqera-enterprise/v25.1.md +++ b/changelog/seqera-enterprise/v25.1.md @@ -107,11 +107,13 @@ According to the [24.10.0](https://github.com/nextflow-io/nextflow/releases/tag/ See the [Nextflow 24.10 migration guide](https://www.nextflow.io/docs/latest/migrations/24-10.html) for full details. -**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.1/launch/advanced#pre-and-post-run-scripts): +:::note +The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.1/launch/advanced#pre-and-post-run-scripts): ```bash export NXF_VER=24.10.4 ``` +::: ### Nextflow launcher image From 98b4265224865bac44d0f41ce668237c26b8a8c6 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Fri, 6 Feb 2026 21:22:07 +0200 Subject: [PATCH 3/3] Update v25.2.md Signed-off-by: Justine Geffen --- changelog/seqera-enterprise/v25.2.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/changelog/seqera-enterprise/v25.2.md b/changelog/seqera-enterprise/v25.2.md index 9e8b81454..0c43317d0 100644 --- a/changelog/seqera-enterprise/v25.2.md +++ b/changelog/seqera-enterprise/v25.2.md @@ -155,11 +155,13 @@ According to the [25.04.0](https://github.com/nextflow-io/nextflow/releases/tag/ See the [Nextflow 25.04 migration guide](https://www.nextflow.io/docs/latest/migrations/25-04.html) for full details. -**Note:** The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.2/launch/advanced#pre-and-post-run-scripts): +:::note +The default Nextflow version can be overridden by setting `NXF_VER` in a [pre-run script](https://docs.seqera.io/platform-enterprise/25.2/launch/advanced#pre-and-post-run-scripts): ```bash export NXF_VER=24.10.4 ``` +::: ### Nextflow launcher image