Merge branch 'master' into rnaseq-full-guide

docusaurus.config.js

@@ -98,7 +98,7 @@ export default async function createConfigAsync() {
           ],
           rehypePlugins: [(await require("rehype-katex")).default],
           editUrl: ({ docPath }) => {
-            return `https://github.com/MultiQC/MultiQC/blob/main/docs${docPath.replace('multiqc_docs/multiqc_repo/docs', '')}`
+            return `https://github.com/MultiQC/MultiQC/blob/main/docs/markdown/${docPath.replace('multiqc_docs/multiqc_repo/docs', '')}`
           },
           sidebarPath: "./multiqc_docs/sidebar.js",
         },

platform_versioned_docs/version-23.3/monitoring/dashboard.mdx

@@ -5,25 +5,25 @@ date: "21 Apr 2023"
 tags: [dashboard, runs, monitoring]
 ---
 
-The Seqera Platform **Dashboard**, accessed from the user menu, provides an overview of runs in your personal and organization workspaces.
+The Seqera Platform **Dashboard**, accessed from the user menu, provides an overview of pipeline runs in your personal and organization workspaces.
 
 ### Filters and summary
 
 The **Dashboard** view defaults to all organizations and workspaces you can access. Select the **View** dropdown menu to filter by specific organizations and workspaces, or to view statistics for your personal workspace only.
 
-You can filter by time, including a custom date range of up to 12 months. To filter the set of runs, select **Filter**. When a filter is applied, the button icon and color changes.
+You can filter by time, including a custom date range of up to 12 months. To filter the set of pipeline runs, select **Filter**. When a filter is applied, the button icon and color changes.
 
 ### Export data
 
 Select **Export data** in the filter panel near the top of the page to export dashboard data, based on the filters you have applied, in a CSV file.
 
-### Runs per organization
+### Pipeline runs per organization
 
-Run totals for your selected filters are displayed for each organization that you have access to.
+Pipeline run totals for your selected filters are displayed for each organization that you have access to.
 
-Depending on the filter selected, each card details a separate workspace or organization. Total runs for each organization are arranged by workspace and status.
+Depending on the filter selected, each card details a separate workspace or organization. Total pipeline runs for each organization are arranged by workspace and status.
 
 For a detailed view of runs, you can do one of the following:
 
-- Select a run integer value in the table to navigate to a run list filtered by the status and time range selected.
-- Select a workspace name in the table to navigate to a run list filtered by the workspace selected.
+- Select a pipeline run integer value in the table to navigate to a list filtered by the status and time range selected.
+- Select a workspace name in the table to navigate to a list filtered by the workspace selected.

platform_versioned_docs/version-23.4/cli/installation.mdx

@@ -95,14 +95,16 @@ source <(tw generate-completion)
 If you are using a Private CA SSL certificate not recognized by the default Java certificate authorities, use a [custom](https://www.baeldung.com/jvm-certificate-store-errors) `cacerts` store:
 
 ```bash
-tw -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts info
+tw -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password> info
 ```
 
-You can rename the binary to `tw-binary` and create a `tw` script to automatically include the custom `cacerts` store in every session:
+Replace `<your-password>` with your keystore password. If you did not set a password when creating the keystore, include the default keystore password `changeit` in the command above. 
+
+You can also rename the binary to `tw-binary` and create a `tw` script to automatically include the custom `cacerts` store in every session:
 
 ```bash
 #!/usr/bin/env bash
-tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts $@
+tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password> $@
 ```
 
 ### Build binary development versions

platform_versioned_docs/version-23.4/monitoring/dashboard.mdx

@@ -1,29 +1,29 @@
 ---
 title: "Dashboard"
-description: "View run status overview in Seqera Platform."
+description: "View pipeline run status overview in Seqera Platform."
 date: "21 Apr 2023"
 tags: [dashboard, runs, monitoring]
 ---
 
-The Seqera Platform **Dashboard**, accessed from the user menu, provides an overview of runs in your personal and organization workspaces.
+The Seqera Platform **Dashboard**, accessed from the user menu, provides an overview of pipeline runs in your personal and organization workspaces.
 
 ### Filters and summary
 
 The **Dashboard** view defaults to all organizations and workspaces you can access. Select the **View** dropdown menu to filter by specific organizations and workspaces, or to view statistics for your personal workspace only.
 
-You can filter by time, including a custom date range of up to 12 months. To filter the set of runs, select **Filter**. When a filter is applied, the button icon and color changes.
+You can filter by time, including a custom date range of up to 12 months. To filter the set of pipeline runs, select **Filter**. When a filter is applied, the button icon and color changes.
 
 ### Export data
 
 Select **Export data** in the filter panel near the top of the page to export dashboard data, based on the filters you have applied, in a CSV file.
 
-### Runs per organization
+### Pipeline runs per organization
 
-Run totals for your selected filters are displayed for each organization that you have access to.
+Pipeline run totals for your selected filters are displayed for each organization that you have access to.
 
-Depending on the filter selected, each card details a separate workspace or organization. Total runs for each organization are arranged by workspace and status.
+Depending on the filter selected, each card details a separate workspace or organization. Total pipeline runs for each organization are arranged by workspace and status.
 
-For a detailed view of runs, you can do one of the following:
+For a detailed view of pipeline runs, you can do one of the following:
 
-- Select a run integer value in the table to navigate to a run list filtered by the status and time range selected.
-- Select a workspace name in the table to navigate to a run list filtered by the workspace selected.
+- Select a pipeline run integer value in the table to navigate to a list filtered by the status and time range selected.
+- Select a workspace name in the table to navigate to a list filtered by the workspace selected.

platform_versioned_docs/version-24.1/cli/installation.mdx

@@ -95,14 +95,16 @@ source <(tw generate-completion)
 If you are using a Private CA SSL certificate not recognized by the default Java certificate authorities, use a [custom](https://www.baeldung.com/jvm-certificate-store-errors) `cacerts` store:
 
 ```bash
-tw -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts info
+tw -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password> info
 ```
 
-You can rename the binary to `tw-binary` and create a `tw` script to automatically include the custom `cacerts` store in every session:
+Replace `<your-password>` with your keystore password. If you did not set a password when creating the keystore, include the default keystore password `changeit` in the command above. 
+
+You can also rename the binary to `tw-binary` and create a `tw` script to automatically include the custom `cacerts` store in every session:
 
 ```bash
 #!/usr/bin/env bash
-tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts $@
+tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password> $@
 ```
 
 ### Build binary development versions

platform_versioned_docs/version-24.1/enterprise/data-studios.mdx

@@ -35,14 +35,14 @@ You can configure which organizational workspaces have access to Data Studios. T
 
 Each of the provided Data Studios environments includes a particular version of the underlying data analytics software package.
 
-To quickly identify which version of the software an image includes, the version string for each container is in the form of `<software_version>-<seqera_version>`. For example, if the version string for the RStudio Server is `4.4.1-0.7.1`, version `4.4.1` is the RStudio version and `0.7.1` is the version of this Seqera-built container image.
+To quickly identify which version of the software an image includes, the version string for each container is in the form of `<software_version>-<seqera_version>`. For example, if the version string for the RStudio Server is `4.4.1-0.7.4`, version `4.4.1` is the RStudio version and `0.7.4` is the version of this Seqera-built container image.
 
 The latest environment versions are listed below:
 
-- JupyterLab: `public.cr.seqera.io/platform/data-studio-jupyter:4.1.5-0.7.1`
-- RStudio Server: `public.cr.seqera.io/platform/data-studio-rstudio:4.4.1-0.7.1`
-- Visual Studio Code: `public.cr.seqera.io/platform/data-studio-vscode:1.83.0-0.7.1`
-- Xpra: `public.cr.seqera.io/platform/data-studio-xpra:6.0-r0-1-0.7.1`
+- JupyterLab: `public.cr.seqera.io/platform/data-studio-jupyter:4.1.5-0.7.4`
+- RStudio Server: `public.cr.seqera.io/platform/data-studio-rstudio:4.4.1-0.7.4`
+- Visual Studio Code: `public.cr.seqera.io/platform/data-studio-vscode:1.83.0-0.7.4`
+- Xpra: `public.cr.seqera.io/platform/data-studio-xpra:6.0-r0-1-0.7.4`
 
 ## Docker Compose
 

platform_versioned_docs/version-24.1/monitoring/dashboard.mdx

@@ -1,29 +1,56 @@
 ---
 title: "Dashboard"
-description: "View run status overview in Seqera Platform."
+description: "View pipeline run status overview in Seqera Platform."
 date: "21 Apr 2023"
-tags: [dashboard, runs, monitoring]
+tags: [dashboard, pipeline runs, monitoring]
 ---
 
-The Seqera Platform **Dashboard**, accessed from the user menu, provides an overview of runs in your personal and organization workspaces.
+The Seqera Platform **Dashboard** is accessed from the user menu and provides an overview of:
 
-### Filters and summary
+- Pipeline runs in your personal and organization workspaces.
+- Data studio sessions in your organization workspaces only.
+
+## Pipeline runs
 
-The **Dashboard** view defaults to all organizations and workspaces you can access. Select the **View** dropdown menu to filter by specific organizations and workspaces, or to view statistics for your personal workspace only.
+You can explore the status of pipeline runs in your personal and in organizational workspaces. On the **Dashboard** page, select **Pipeline Runs**.
+
+### Filters and summary
 
-You can filter by time, including a custom date range of up to 12 months. To filter the set of runs, select **Filter**. When a filter is applied, the button icon and color changes.
+The **Dashboard** view defaults to all organizations and workspaces you can access. Select the **View** dropdown menu to filter by specific organizations and workspaces, or to view statistics for your personal workspace only. You can filter by time, including a custom date range of up to 12 months. To filter the set of pipeline runs, select **Filter**. When a filter is applied, the button icon and color changes.
 
 ### Export data
 
 Select **Export data** in the filter panel near the top of the page to export dashboard data, based on the filters you have applied, in a CSV file.
 
-### Runs per organization
+### Pipeline runs per organization
+
+The pipeline run totals for your selected filters are displayed for each organization that you have access to.
+
+Depending on the filter selected, each card details a separate workspace or organization. Total pipeline runs for each organization are arranged by workspace and status.
+
+For a detailed view, you can do one of the following:
+
+- Select a pipeline run integer value in the table to navigate to a pipeline run list filtered by the status and time range selected.
+- Select a workspace name in the table to navigate to a pipeline run list filtered by the workspace selected.
 
-Run totals for your selected filters are displayed for each organization that you have access to.
+## Data Studios
+
+You can explore the status of data studio sessions in your organizational workspaces. On the **Dashboard** page, select **Data Studios**. The following statuses are listed with the number of data studio sessions in each status:
+
+- `Running`
+- `Errored`
+- `Starting`
+- `Stopping`
+- `Stopped`
+
+### Filters and summary
+
+The **Dashboard** view defaults to all organizations and workspaces you can access. Select the **View** dropdown menu to filter by organizations and workspaces. Select a status in the table to navigate to a list filtered by the status selected.
+
+### Export data
 
-Depending on the filter selected, each card details a separate workspace or organization. Total runs for each organization are arranged by workspace and status.
+Select **Export data** in the view panel near the top of the page to export a CSV of the dashboard data for the selected organizations and workspaces.
 
-For a detailed view of runs, you can do one of the following:
 
-- Select a run integer value in the table to navigate to a run list filtered by the status and time range selected.
-- Select a workspace name in the table to navigate to a run list filtered by the workspace selected.
+<!-- links -->
+[ds]: ../data/data-studios.mdx

src/theme/DocSidebar/Desktop/ProductSwitcher/VersionSwitcher.tsx

@@ -44,6 +44,10 @@ const VersionSwitcher = ({ isOpen, setIsOpen }) => {
     (version) => version.label !== currentVersion.label,
   );
 
+  // Extract the part of the URL after the current version
+  const currentVersionPrefix = `/platform/${currentVersion.label}`;
+  const urlSuffix = location.pathname.replace(currentVersionPrefix, "");
+
   return (
     <>
       <button
@@ -67,7 +71,7 @@ const VersionSwitcher = ({ isOpen, setIsOpen }) => {
           {items?.map((version) => (
             <Link
               key={version.name}
-              to={version.path}
+              to={`${version.path}${urlSuffix}`} // Append the suffix to the version path
               className={styles.item}
               onClick={() => handleSelectVersion(version.name)}
             >

src/theme/DocSidebar/Desktop/styles.module.css

@@ -3,10 +3,10 @@
   margin-top: unset !important;
 }
 [data-theme="light"] :global(.theme-doc-sidebar-container) {
-  background: rgba(0, 0, 0, 0.02);
+  background: rgb(249, 249, 249);
 }
 [data-theme="dark"] :global(.theme-doc-sidebar-container) {
-  background: rgba(255, 255, 255, 0.08);
+  background: rgb(27, 24, 35);
 }
 
 .sidebar {
@@ -32,6 +32,9 @@
   height: 15px;
   background: linear-gradient(180deg, rgba(249,249,249,1) 0%, rgba(249,249,249,0) 100%);
 }
+[data-theme="dark"] .sidebarHeaderFade {
+  background: linear-gradient(180deg, rgba(27, 24, 35,0.5) 0%, rgba(27, 24, 35,0) 100%) ;
+}
 .sidebarNav {
   margin-top: -15px;
   padding: 30px;

src/theme/Navbar/Layout/styles.custom.module.css

@@ -1,9 +1,6 @@
 html {
   @media (min-width: 997px) {
     scroll-padding-top: 110px;
-    & :global(.theme-doc-toc-desktop) {
-      top: calc(var(--ifm-navbar-height) + 6.5rem) !important;
-    }
   }
 }
 .siteHeader {