Merge branch 'master' into PLAT-330_Azure_docs

Author: adamrtalbot

.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 +1,31 @@
+name: Links
+
+# https://github.com/lycheeverse/lychee-action
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+  # Run on Sunday only
+  schedule:
+  - cron: "00 18 * * 6"
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1
+        # --verbose --no-progress
+        with:
+          args: --base . -v -n -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

.gitignore

@@ -7,6 +7,7 @@
 # Generated files
 .docusaurus
 .cache-loader
+.cache
 
 # Misc
 .env

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "wave_docs/wave_repo"]
 	path = wave_docs/wave_repo
 	url = https://github.com/seqeralabs/wave
+[submodule "multiqc_docs/multiqc_repo"]
+	path = multiqc_docs/multiqc_repo
+	url = https://github.com/MultiQC/MultiQC

README.md

@@ -52,6 +52,9 @@ export default async function createConfigAsync() {
             trackingID: "G-NR1CNM213G",
             anonymizeIP: true,
           },
+          googleTagManager: {
+            containerId: "GTM-MBCJKK4",
+          },
         },
       ],
     ],
@@ -72,7 +75,7 @@ export default async function createConfigAsync() {
           editUrl: "https://github.com/seqeralabs/docs/tree/master/",
           sidebarPath: false,
           versions: {
-            // Force path to be /platform/23.3.0 instead of /platform
+            // Force path to be /platform/24.1 instead of /platform
             // (Applies to latest version only)
             [platform_latest_version]: {
               label: platform_latest_version,
@@ -82,6 +85,24 @@ export default async function createConfigAsync() {
         },
       ],
       [
+        "@docusaurus/plugin-content-docs",
+        {
+          id: "multiqc",
+          routeBasePath: "/multiqc",
+          path: "multiqc_docs/multiqc_repo/docs/markdown",
+          remarkPlugins: [
+            (await import("remark-code-import")).default,
+            (await require("remark-math")).default,
+            (await import("docusaurus-remark-plugin-tab-blocks")).default,
+            (await require("remark-yaml-to-table")).default,
+          ],
+          rehypePlugins: [(await require("rehype-katex")).default],
+          editUrl: ({ docPath }) => {
+            return `https://github.com/MultiQC/MultiQC/blob/main/docs${docPath.replace('multiqc_docs/multiqc_repo/docs', '')}`
+          },
+          sidebarPath: "./multiqc_docs/sidebar.js",
+        },
+      ],      [
         "@docusaurus/plugin-content-docs",
         {
           id: "fusion",
@@ -166,10 +187,9 @@ export default async function createConfigAsync() {
             target: "_blank",
           },
           {
-            to: "https://multiqc.info/docs/",
-            html: 'MultiQC <svg width="12" height="12" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU" style="margin-left:4px;opacity:0.6;"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg>',
+            to: "/multiqc/",
+            label: "MultiQC",
             position: "left",
-            target: "_blank",
           },
           {
             to: "/wave/",

docusaurus.config.js

@@ -0,0 +1,10 @@
+# https://lychee.cli.rs/usage/config/
+scheme = ["https", "http"]
+exclude = [
+  '^https://portal.azure.com/',
+  '^https://gitlab.com/profile/personal_access_tokens'
+]
+exclude_path = [
+  "^.+/README.mdx",
+  "^.+/_todo.mdx"
+]