Merge branch 'master' into port-cli-docs

.github/workflows/check-internal-links.yml

@@ -0,0 +1,29 @@
+name: "Internal link checking"
+
+on: [pull_request]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  check-internal-links:
+    runs-on: ubuntu-latest
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Check out repo
+        uses: actions/checkout@v2
+      # Node is required for npm
+      - name: Set up Node
+        uses: actions/setup-node@v2
+        with:
+          node-version: "18"
+      - name: Pull & update submodules recursively
+        run: |
+          git submodule update --init --recursive
+      # Fail the build in PRs, but not for Netlify previews or production builds
+      - name: Replace credentials
+        run: |
+          sed -Ei 's/onBroken([A-Za-z]+): "warn"/onBroken\1: "throw"/g' docusaurus.config.js
+      # Install and build Docusaurus website
+      - name: Build Docusaurus website
+        run: |
+          npm install
+          npm run build

.github/workflows/links.yml

@@ -0,0 +1,29 @@
+name: Links
+
+# https://github.com/lycheeverse/lychee-action
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+  schedule:
+    - cron: "00 18 * * *"
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1
+        with:
+          args: --base . --verbose --no-progress -s https -s http './**/*.mdx'
+
+      - name: Create Issue From File
+        if: env.lychee_exit_code != 0
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: Link Checker Report
+          content-filepath: ./lychee/out.md
+          labels: report, automated issue

fusion_docs/guide.mdx

@@ -6,14 +6,15 @@ title: User guide
 
 Fusion is a virtual, lightweight, distributed file system designed to optimise the data access of Nextflow data pipelines.
 
-Fusion enables seamless filesystem I/O to cloud object stores via a standard POSIX interface resulting in simpler
-pipeline logic and faster, more efficient pipeline execution.
+Fusion enables seamless filesystem I/O to cloud object stores via a standard POSIX interface resulting in simpler pipeline logic and faster, more efficient pipeline execution.
+
+:::note
+Fusion requires a license for use beyond limited testing and validation within Seqera Platform or directly within Nextflow. [Contact Seqera](https://seqera.io/contact-us/) for more details.
+:::
 
 ## Getting started
 
-Fusion smoothly integrates with Nextflow and does not require any installation or change in pipeline code.
-It only requires to use of container runtime or a container computing service such as Kubernetes, AWS Batch and
-Google Cloud Batch.
+Fusion smoothly integrates with Nextflow and does not require any installation or change in pipeline code. It only requires to use of container runtime or a container computing service such as Kubernetes, AWS Batch, or Google Cloud Batch.
 
 :::note
 

fusion_docs/index.mdx

@@ -11,6 +11,10 @@ Fusion is a virtual, lightweight, distributed file system that bridges the gap b
 storage. Fusion enables seamless filesystem I/O to cloud object stores via a standard POSIX interface resulting in
 simpler pipeline logic and faster, more efficient pipeline execution.
 
+:::note 
+Fusion requires a license for use beyond limited testing and validation within Seqera Platform or directly within Nextflow. [Contact Seqera](https://seqera.io/contact-us/) for more details.
+:::
+
 ## Features
 
 ### Transparent, automated installation

platform_versioned_docs/version-22.4.0/compute-envs/aws-batch.mdx

@@ -126,7 +126,7 @@ Once the AWS resources are set up, we can add a new **AWS Batch** environment in
     :::
 
     :::note
-    From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx/#container-registry-credentials) tab.
+    From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx) tab.
     :::
 
 7.  Select a **Region**, for example "eu-west-1 - Europe (Ireland)".

platform_versioned_docs/version-22.4.0/compute-envs/azure-batch.mdx

@@ -117,7 +117,7 @@ Once the Azure resources are set up, we can add a new **Azure Batch** environmen
    :::
 
    :::note
-   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx/#container-registry-credentials) tab.
+   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx) tab.
    :::
 
 7. Select a **Region**, for example "eastus (East US)".

platform_versioned_docs/version-22.4.0/compute-envs/eks.mdx

@@ -11,7 +11,7 @@ Tower offers native support for AWS EKS clusters and streamlines the deployment
 
 ## Requirements
 
-You need to have an EKS cluster up and running. Make sure you have followed the [cluster preparation](../k8s/#cluster-preparation) instructions to create the cluster resources required by Tower. In addition to the generic Kubernetes instructions, you will need to make a few modifications specific to EKS.
+You need to have an EKS cluster up and running. Make sure you have followed the [cluster preparation](../compute-envs/k8s.mdx#cluster-preparation) instructions to create the cluster resources required by Tower. In addition to the generic Kubernetes instructions, you will need to make a few modifications specific to EKS.
 
 **Assign service account role to IAM user.** You will need to assign the service role with an AWS user that will be used by Tower to access the EKS cluster.
 
@@ -67,7 +67,7 @@ For more details, refer to the [AWS documentation](https://docs.aws.amazon.com/e
    :::
 
    :::note
-   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx/#container-registry-credentials) tab.
+   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx) tab.
    :::
 
 5. Select a **Region**, for example "eu-west-1 - Europe (Ireland)".

platform_versioned_docs/version-22.4.0/compute-envs/gke.mdx

@@ -11,9 +11,9 @@ Tower offers native support for Google GKE clusters and streamlines the deployme
 
 ### Requirements
 
-Refer to the [Google Cloud](../google-cloud/#configure-google-cloud) section for instructions on how to set up your Google Cloud account and any other services (e.g. Cloud Storage) that you intend to use.
+Refer to the [Google Cloud](./google-cloud-batch.mdx#configure-google-cloud) section for instructions on how to set up your Google Cloud account and any other services (e.g. Cloud Storage) that you intend to use.
 
-You need to have a GKE cluster up and running. Make sure you have followed the [cluster preparation](../k8s/#cluster-preparation) instructions to create the cluster resources required by Tower. In addition to the generic Kubernetes instructions, you will need to make a few modifications specific to GKE.
+You need to have a GKE cluster up and running. Make sure you have followed the [cluster preparation](../compute-envs/k8s.mdx#cluster-preparation) instructions to create the cluster resources required by Tower. In addition to the generic Kubernetes instructions, you will need to make a few modifications specific to GKE.
 
 **Assign service account role to IAM user.** You will need to grant the cluster access to the service account used to authenticate the Tower compute environment. This can be done by updating the _role binding_ as shown below:
 
@@ -59,7 +59,7 @@ For more details, refer to the [Google documentation](https://cloud.google.com/k
    :::
 
    :::note
-   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx/#container-registry-credentials.mdx) tab.
+   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx) tab.
    :::
 
 7. Select the **Location** of your GKE cluster.

platform_versioned_docs/version-22.4.0/compute-envs/google-cloud-lifesciences.mdx

@@ -123,7 +123,7 @@ To create a new compute environment for Google Cloud in Tower:
    :::
 
    :::note
-   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx/#container-registry-credentials) tab.
+   From version 22.3, Tower supports the use of credentials for container registry services. These credentials can be created from the [Credentials](../credentials/overview.mdx) tab.
    :::
 
 7. Select the [**Region** and **Zones**](https://cloud.google.com/compute/docs/regions-zones#available) where you'd like to execute pipelines. You can leave the **Location** empty and the Cloud Life Sciences API will use the closest available location.

platform_versioned_docs/version-22.4.0/compute-envs/k8s.mdx

@@ -9,7 +9,7 @@ description: "Step-by-step instructions to set up a Nextflow Tower compute envir
 
 Tower streamlines the deployment of Nextflow pipelines into Kubernetes both for cloud-based and on-prem clusters.
 
-The following instructions are for a **generic Kubernetes** distribution. If you are using [Amazon EKS](../eks/) or [Google GKE](../gke/), see the corresponding documentation pages.
+The following instructions are for a **generic Kubernetes** distribution. If you are using [Amazon EKS](eks.mdx) or [Google GKE](gke.mdx), see the corresponding documentation pages.
 
 ### Cluster Preparation
 

platform_versioned_docs/version-22.4.0/data-privacy/overview.mdx

@@ -91,7 +91,7 @@ The following metadata fields are collected and stored by the Tower backend duri
 
 | Name           | Description                                                                                    |
 | -------------- | ---------------------------------------------------------------------------------------------- |
-| `attempt`      | Number of execution attempt of the task                                                        |
+| `attempt`      | Number of Nextflow execution attempts of the task                                              |
 | `cloud_zone`   | Cloud zone where the task execution was allocated                                              |
 | `complete`     | Task execution completion timestamp                                                            |
 | `container`    | Container image name used to execute the task                                                  |

platform_versioned_docs/version-22.4.0/orgs-and-teams/workspace-management.mdx

@@ -11,7 +11,7 @@ description: "Manage users and teams for an organization."
 Organizations consist of members, while workspaces consist of participants.
 
 :::note
-A workspace participant may be a member of the workspace organization or a collaborator within that workspace only. Collaborators count toward the total number of workspace participants. See [Usage limits](/docs/limits/limits.mdx).
+A workspace participant may be a member of the workspace organization or a collaborator within that workspace only. Collaborators count toward the total number of workspace participants. See [Usage limits](../limits/limits.mdx).
 :::
 
 ### Create a new workspace

platform_versioned_docs/version-22.4.0/resource-labels/overview.mdx

@@ -111,7 +111,7 @@ When the compute environment is created with Forge, the following resources will
 
 At execution time, when the jobs are submitted to Batch, the requests are set up to propagate tags to all the instances created by the head job.
 
-The [`forge-policy.json`](/docs/_templates/aws-batch/forge-policy.json) file contains the roles needed for Batch Forge-created AWS compute environments to tag AWS resources. Specifically, the required roles are `iam:TagRole`, `iam:TagInstanceProfile`, and `batch:TagResource`.
+The [`forge-policy.json`](../_templates/aws-batch/forge-policy.json) file contains the roles needed for Batch Forge-created AWS compute environments to tag AWS resources. Specifically, the required roles are `iam:TagRole`, `iam:TagInstanceProfile`, and `batch:TagResource`.
 
 To view and manage the resource labels applied to AWS resources by Tower and Nextflow, navigate to the [AWS Tag Editor](https://docs.aws.amazon.com/tag-editor/latest/userguide/find-resources-to-tag.html)(as an administrative user) and follow these steps:
 

platform_versioned_docs/version-22.4.0/supported_software/fusion/fusion.mdx

@@ -15,10 +15,10 @@ To enable Fusion in Tower:
 
 - Use Nextflow version `22.10.0` or later. The latest version of Nextflow is used in Tower by default, but a particular version can be specified using `NXF_VER` in the Nextflow config file field (**Advanced options -> Nextflow config file** under Pipeline settings on the launch page).
 
-- Enable the [Wave containers service](https://www.nextflow.io/docs/latest/wave.html#wave-page) during [AWS Batch](/docs/compute-envs/aws-batch.mdx) compute environment creation.
+- Enable the [Wave containers service](https://www.nextflow.io/docs/latest/wave.html#wave-page) during [AWS Batch](../../compute-envs/aws-batch.mdx) compute environment creation.
 
 - Select **Enable Fusion v2** during compute environment creation.
 
 - (Optional) Select **Enable fast instance storage** to make use of NVMe instance storage to further increase performance.
 
-See the [AWS Batch](/docs/compute-envs/aws-batch.mdx#) compute environment page for detailed instructions.
+See the [AWS Batch](../../compute-envs/aws-batch.mdx) compute environment page for detailed instructions.

platform_versioned_docs/version-23.1.0/data-privacy/overview.mdx

@@ -92,7 +92,7 @@ The following metadata fields are collected and stored by the Tower backend duri
 
 | Name           | Description                                                                                    |
 | -------------- | ---------------------------------------------------------------------------------------------- |
-| `attempt`      | Number of execution attempt of the task                                                        |
+| `attempt`      | Number of Nextflow execution attempts of the task                                              |
 | `cloud_zone`   | Cloud zone where the task execution was allocated                                              |
 | `complete`     | Task execution completion timestamp                                                            |
 | `container`    | Container image name used to execute the task                                                  |

platform_versioned_docs/version-23.1.0/enterprise/_templates/k8s/ingress.aks.yml

@@ -10,6 +10,9 @@ spec:
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: frontend
-              servicePort: 80
+              service:
+                name: frontend
+                port:
+                  number: 80

platform_versioned_docs/version-23.1.0/enterprise/_templates/k8s/ingress.eks.yml

@@ -17,14 +17,20 @@ metadata:
       access_logs.s3.prefix=YOUR-LOGS-PREFIX
 spec:
   rules:
-    - host: YOUR-TOWER-HOST-NAME
+    - host: <YOUR-TOWER-HOST-NAME>
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: ssl-redirect
-              servicePort: use-annotation
+              service:
+                name: ssl-redirect
+                port:
+                  name: use-annotation
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: frontend
-              servicePort: 80
+              service:
+                name: frontend
+                port:
+                  number: 80

platform_versioned_docs/version-23.1.0/enterprise/release_notes/changelog.mdx

@@ -412,7 +412,7 @@ tags: [changelog]
 - Fix Unable to download execution log from a workflow with working directory specified just as "bucket" name [d025917c]
 - Fix Prevent the creation of Spot fleet role [95acea2c]
 - Fix Prevent deletion of an active workflow run [ba1f1ce9]
-- Fix Prevent XSS attacks when uploading a datatable file [#2944](6d98210c)
+- Fix Prevent XSS attacks when uploading a datatable file [#2944] (6d98210c)
 - 8759d92e - Validate launch/re-launch action depending the user role
 - d6113805 - Bump base image nf-jdk:corretto-11.0.14_2 [ci fast]
 

platform_versioned_docs/version-23.1.0/orgs-and-teams/workspace-management.mdx

@@ -12,7 +12,7 @@ tags: [workspaces, teams, users, administration]
 Organizations consist of members, while workspaces consist of participants.
 
 :::note
-A workspace participant may be a member of the workspace organization or a collaborator within that workspace only. Collaborators count toward the total number of workspace participants. See [Usage limits](/docs/limits/limits.mdx).
+A workspace participant may be a member of the workspace organization or a collaborator within that workspace only. Collaborators count toward the total number of workspace participants. See [Usage limits](../limits/limits.mdx).
 :::
 
 ### Create a new workspace

platform_versioned_docs/version-23.2.0/credentials/agent_credentials.mdx

@@ -5,7 +5,7 @@ date: "21 Apr 2023"
 tags: [agent, credentials]
 ---
 
-[Tower Agent](../agent.mdx) enables Tower to launch pipelines on HPC clusters that do not allow direct access through an SSH client. Tower Agent authenticates a secure connection with Tower using a Tower Agent credential.
+[Tower Agent](../supported_software/agent/agent.mdx) enables Tower to launch pipelines on HPC clusters that do not allow direct access through an SSH client. Tower Agent authenticates a secure connection with Tower using a Tower Agent credential.
 
 ### Tower Agent sharing
 

platform_versioned_docs/version-23.2.0/data-privacy/overview.mdx

@@ -92,7 +92,7 @@ The following metadata fields are collected and stored by the Tower backend duri
 
 | Name           | Description                                                                                    |
 | -------------- | ---------------------------------------------------------------------------------------------- |
-| `attempt`      | Number of execution attempt of the task                                                        |
+| `attempt`      | Number of Nextflow execution attempts of the task                                              |
 | `cloud_zone`   | Cloud zone where the task execution was allocated                                              |
 | `complete`     | Task execution completion timestamp                                                            |
 | `container`    | Container image name used to execute the task                                                  |

platform_versioned_docs/version-23.2.0/enterprise/_templates/k8s/ingress.aks.yml

@@ -10,6 +10,9 @@ spec:
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: frontend
-              servicePort: 80
+              service:
+                name: frontend
+                port:
+                  number: 80

platform_versioned_docs/version-23.2.0/enterprise/_templates/k8s/ingress.eks.yml

@@ -17,14 +17,20 @@ metadata:
       access_logs.s3.prefix=YOUR-LOGS-PREFIX
 spec:
   rules:
-    - host: YOUR-TOWER-HOST-NAME
+    - host: <YOUR-TOWER-HOST-NAME>
       http:
         paths:
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: ssl-redirect
-              servicePort: use-annotation
+              service:
+                name: ssl-redirect
+                port:
+                  name: use-annotation
           - path: /*
+            pathType: ImplementationSpecific
             backend:
-              serviceName: frontend
-              servicePort: 80
+              service:
+                name: frontend
+                port:
+                  number: 80