Merge branch 'master' into justinegeffen-patch-1

docusaurus.config.js

@@ -32,6 +32,10 @@ export default async function createConfigAsync() {
       locales: ["en"],
     },
 
+    future: {
+      experimental_faster: true,
+    },
+
     presets: [
       [
         "classic",

package.json

@@ -19,10 +19,11 @@
     "markdownlint": "markdownlint-cli2 'platform_versioned_docs/**/*.mdx' 'wave_docs/**/*.mdx' 'fusion_docs/**/*.mdx' --config .markdownlint-cli2.cjs"
   },
   "dependencies": {
-    "@docusaurus/core": "^3.5.2",
-    "@docusaurus/plugin-google-gtag": "^3.5.2",
-    "@docusaurus/plugin-google-tag-manager": "^3.5.2",
-    "@docusaurus/preset-classic": "^3.5.2",
+    "@docusaurus/core": "^3.6.0",
+    "@docusaurus/faster": "^3.5.2",
+    "@docusaurus/plugin-google-gtag": "^3.6.0",
+    "@docusaurus/plugin-google-tag-manager": "^3.6.0",
+    "@docusaurus/preset-classic": "^3.6.0",
     "@mdx-js/react": "^3.0.0",
     "clsx": "^1.2.1",
     "docusaurus-remark-plugin-tab-blocks": "^3.1.0",
@@ -40,8 +41,8 @@
     "remark-yaml-to-table": "github:seqeralabs/remark-yaml-to-table"
   },
   "devDependencies": {
-    "@docusaurus/eslint-plugin": "^3.5.2",
-    "@docusaurus/module-type-aliases": "^3.5.2",
+    "@docusaurus/eslint-plugin": "^3.6.0",
+    "@docusaurus/module-type-aliases": "^3.6.0",
     "@tsconfig/docusaurus": "^1.0.5",
     "autoprefixer": "^10.4.16",
     "dotenv": "^16.3.1",
@@ -71,6 +72,6 @@
     ]
   },
   "engines": {
-    "node": ">=18.00"
+    "node": ">=18"
   }
 }

platform_versioned_docs/version-23.4/getting-started/workspace-setup.mdx

@@ -19,7 +19,7 @@ Organizations are the top-level structure and contain workspaces, members, and t
     - The **Full name** of the organization. 
     - A **Description** of the organization to provide contextual information that may be helpful to other organization members. 
     - The organization's **Location**.
-    - The organization's **Wesbite URL**. 
+    - The organization's **Website URL**. 
     - Drag and drop or upload an image to be used as the organization's **Logo** in Platform. 
 1. Select **Add**. 
 

platform_versioned_docs/version-24.1/getting-started/workspace-setup.mdx

@@ -19,7 +19,7 @@ Organizations are the top-level structure and contain workspaces, members, and t
     - The **Full name** of the organization. 
     - A **Description** of the organization to provide contextual information that may be helpful to other organization members. 
     - The organization's **Location**.
-    - The organization's **Wesbite URL**. 
+    - The organization's **Website URL**. 
     - Drag and drop or upload an image to be used as the organization's **Logo** in Platform. 
 1. Select **Add**. 
 

platform_versioned_docs/version-24.2/compute-envs/aws-batch.mdx

@@ -179,7 +179,10 @@ Batch Forge automatically creates resources that you may be charged for in your
 1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**.
 1. Configure any advanced options described in the next section, as needed.
 1. Select **Create** to finalize the compute environment setup. It will take a few seconds for all the AWS resources to be created before you are ready to launch pipelines.
@@ -324,7 +327,10 @@ Your Seqera compute environment uses resources that you may be charged for in yo
 1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    ::: 
 1. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**.
 1. Configure any advanced options described in the next section, as needed.
 1. Select **Create** to finalize the compute environment setup.

platform_versioned_docs/version-24.2/compute-envs/azure-batch.mdx

@@ -40,7 +40,7 @@ A resource group can be created while creating an Azure Storage account or Azure
 :::
 
 1. Log in to your Azure account, go to the [Create Resource group][az-create-rg] page, and select **Create new resource group**.
-1. Enter a name for the resource group, such as _seqerarg_.
+1. Enter a name for the resource group, such as _seqeracompute_.
 1. Choose the preferred region.
 1. Select **Review and Create** to proceed.
 1. Select **Create**.
@@ -234,7 +234,12 @@ Create a Batch Forge Azure Batch compute environment:
 1. Enable **Dispose resources** for Seqera to automatically delete the Batch pool if the compute environment is deleted on the platform.
 1. Select or create [**Container registry credentials**](../credentials/azure_registry_credentials.mdx) to authenticate a registry (used by the [Wave containers](https://www.nextflow.io/docs/latest/wave.html) service). It is recommended to use an [Azure Container registry](https://azure.microsoft.com/en-gb/products/container-registry) within the same region for maximum performance.
 1. Apply [**Resource labels**](../resource-labels/overview.mdx). This will populate the **Metadata** fields of the Azure Batch pool.
-1. Expand **Staging options** to include optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre-and-post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
+1. Expand **Staging options** to include:
+    - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**.
 1. Configure any advanced options you need:
     - Use **Jobs cleanup policy** to control how Nextflow process jobs are deleted on completion. Active jobs consume the quota of the Azure Batch account. By default, jobs are terminated by Nextflow and removed from the quota when all tasks succesfully complete. If set to _Always_, all jobs are deleted by Nextflow after pipeline completion. If set to _Never_, jobs are never deleted. If set to _On success_, successful tasks are removed but failed tasks will be left for debugging purposes.
@@ -301,7 +306,10 @@ Create a manual Seqera Azure Batch compute environment:
 1. Apply [**Resource labels**](../resource-labels/overview.mdx). This will populate the **Metadata** fields of the Azure Batch pool.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
     :::info
     To use managed identities, Platform requires Nextflow version 24.06.0-edge or later. Add `export NXF_VER=24.06.0-edge` to the **Global Nextflow config** field for your compute environment to use this Nextflow version by default. 
     :::

platform_versioned_docs/version-24.2/compute-envs/eks.mdx

@@ -85,7 +85,10 @@ After you have prepared your Kubernetes cluster and assigned a service account r
 1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**.
 1. Configure any advanced options described in the next section, as needed.
 1. Select **Create** to finalize the compute environment setup.

platform_versioned_docs/version-24.2/compute-envs/gke.mdx

@@ -79,7 +79,10 @@ After you've prepared your Kubernetes cluster and granted cluster access to your
 1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. Specify custom **Environment variables** for the **Head job** and/or **Compute jobs**.
 1. Configure any advanced options described in the next section, as needed.
 1. Select **Create** to finalize the compute environment setup.

platform_versioned_docs/version-24.2/compute-envs/google-cloud-batch.mdx

@@ -196,12 +196,15 @@ Apply [**Resource labels**][resource-labels] to the cloud resources consumed by
 
 #### Scripting and environment variables
 
-Expand **Staging options** to include:
-  - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-  - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+- Expand **Staging options** to include:
+    - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 
 
-Specify custom **Environment variables** for the head and compute jobs.
+- Specify custom **Environment variables** for the head and compute jobs.
 
 #### Advanced options
 

platform_versioned_docs/version-24.2/compute-envs/google-cloud-lifesciences.mdx

@@ -1,10 +1,14 @@
 ---
-title: "Google Life Sciences"
+title: "Google Life Sciences (deprecated)"
 description: "Instructions to set up Google Life Sciences in Seqera Platform"
 date: "21 Apr 2023"
 tags: [google, gcp, life sciences, compute environment]
 ---
 
+:::info
+Google Cloud Life Sciences is [deprecated](https://cloud.google.com/life-sciences/docs/getting-support) and will no longer be available on Google Cloud after July 8, 2025.
+:::
+
 This guide assumes you have an existing Google Cloud account. Sign up for a free account [here](https://cloud.google.com/). Seqera Platform provides integration to Google Cloud via the [Cloud Life Sciences API](https://cloud.google.com/life-sciences/docs/reference/rest).
 
 This guide is split into two parts:
@@ -123,9 +127,12 @@ You can create multiple credentials in your Seqera workspace. See [Credentials](
 9. You can enable **Preemptible** to use preemptible instances, which have significantly reduced cost compared to on-demand instances.
 10. You can use a **Filestore file system** to automatically mount a Google Filestore volume in your pipelines.
 11. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
-12. Expand **Staging options** to include:
+1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 13. Use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs.
 14. Configure any advanced options you need:
     - Enable **Use Private Address** to ensure that your Google Cloud VMs aren't accessible to the public internet.

platform_versioned_docs/version-24.2/compute-envs/hpc.mdx

@@ -68,7 +68,10 @@ To create a new **HPC** compute environment:
 1. Enter the **Compute queue name**. This is the [default](https://www.nextflow.io/docs/latest/process.html#queue) cluster queue to which the Nextflow job will submit tasks.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. Specify custom **Environment variables** for the head job and/or compute jobs.
 1. Configure any advanced options needed:
     - Use the **Nextflow queue size** to limit the number of jobs that Nextflow can submit to the scheduler at the same time.

platform_versioned_docs/version-24.2/compute-envs/k8s.mdx

@@ -116,7 +116,10 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c
 1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.
 1. Expand **Staging options** to include:
     - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment.
-    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Configuration settings in this field override the same values in the pipeline Nextflow config file. 
+    - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. 
+    :::info
+    Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. 
+    :::
 1. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs.
 1. Configure any advanced options described below, as needed.
 1. Select **Create** to finalize the compute environment setup.

platform_versioned_docs/version-24.2/getting-started/workspace-setup.mdx

@@ -19,7 +19,7 @@ Organizations are the top-level structure and contain workspaces, members, and t
     - The **Full name** of the organization. 
     - A **Description** of the organization to provide contextual information that may be helpful to other organization members. 
     - The organization's **Location**.
-    - The organization's **Wesbite URL**. 
+    - The organization's **Website URL**. 
     - Drag and drop or upload an image to be used as the organization's **Logo** in Platform. 
 1. Select **Add**.