Merge branch 'main' into bytesize_transcript_mentoring

.github/CONTRIBUTING.md

@@ -5,7 +5,8 @@ menu:
   main:
     weight: 10
 ---
-# nf-core/nf-co.re - Contributing Guidelines
+
+# nf-core/website - Contributing Guidelines
 
 Hi there! Many thanks for taking an interest in improving the nf-core website.
 
@@ -43,14 +44,14 @@ Please note that`nf-co.re` website makes use of the `light/dark` mode so it's re
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/nf-co.re, the standard workflow
+If you'd like to write some code for nf-core/website, the standard workflow
 is as follows:
 
 1. Check that there isn't already an issue about your idea in the
-   [nf-core/nf-co.re issues](https://github.com/nf-core/nf-co.re/issues) to avoid
+   [nf-core/website issues](https://github.com/nf-core/website/issues) to avoid
    duplicating work.
    - If there isn't one already, please create one so that others know you're working on this
-2. Fork the [nf-core/nf-co.re repository](https://github.com/nf-core/nf-co.re) to your GitHub account
+2. Fork the [nf-core/website repository](https://github.com/nf-core/website) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
 4. Submit a Pull Request against the `main` branch and wait for the code to be reviewed and merged.
 
@@ -64,4 +65,4 @@ For now, the only test is for Markdown syntax, using the `markdownlint` package.
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/nf-co.re documentation](https://github.com/nf-core/nf-co.re#documentation) and don't hesitate to get in touch on the nf-core `tools` channel on [Slack](https://nf-co.re/join/slack/).
+For further information/help, please consult the [nf-core/website documentation](https://github.com/nf-core/website#documentation) and don't hesitate to get in touch on the nf-core `tools` channel on [Slack](https://nf-co.re/join/slack/).

.github/workflows/build-json-files-and-md-cache.yml

@@ -9,18 +9,20 @@ jobs:
   build-component-json:
     runs-on: ubuntu-latest
     environment: static-file-build
+    if: (github.event_name == 'schedule' && github.repository == 'nf-core/website') || (github.event_name != 'schedule')
 
     steps:
       # Set up the main website repo
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Don't do a shallow clone
+          token: ${{secrets.NF_CORE_BOT_AUTH_TOKEN}} # Needed for pushing back to the repo
 
       # install npm dependencies
       - name: Set up node.js
         uses: actions/setup-node@v3
         with:
-          node-version: 16.x
+          node-version: 18
           cache: 'npm'
       - run: npm install
 
@@ -34,14 +36,60 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.PIPLINE_JSON_BUILD_TOKEN }}
 
-
       - name: make md cache
-        run: node bin/build-cache.js && tar -czvf .cache.tar.gz .cache
+        run: node bin/build-cache.js && tar -cvJf .cache.tar.xz .cache
         env:
           GITHUB_TOKEN: ${{ secrets.CREATE_CACHE_MD_TOKEN }}
 
-      # Commit and push the changes
+      # check lines if too many lines of code have been changed in /public/pipelines.json and /pulic/components.json
+      # also check if .cache.tar.xz is smaller than before (shouldn't happen)
+      - name: check lines
+        run: |
+          diff_output=$(git diff --shortstat public/pipelines.json public/components.json)
+          lines_added=$(echo $diff_output | awk '{print $4}')
+          lines_removed=$(echo $diff_output | awk '{print $6}')
+          changes=$((lines_added - lines_removed))
+
+          if (($changes < -100)) || (($changes > 100)); then
+            file_size_before=$(echo $diff_output | awk '{print $4}')
+            file_size_after=$(echo $diff_output | awk '{print $6}')
+            changes=true
+          fi
+
+          if [ ! $changes ]; then
+            diff_output=$(git diff --stat .cache.tar.xz)
+            file_size_before=$(echo $diff_output | awk '{print $4}')
+            file_size_after=$(echo $diff_output | awk '{print $6}')
+            changes_tmp=$((file_size_before - file_size_after))
+            if ((changes_tmp > 0)); then
+              changes=true
+            else
+              changes=false
+            fi
+          fi
+
+          echo "changes=$changes" >> "$GITHUB_OUTPUT"
+
+      # Commit and push the changes if there are not too many lines changed
       - name: Commit and push changes
-        uses: EndBug/add-and-commit@v9
+        if: ${{ !steps.check_lines.outputs.changes }}
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git status
+          git diff --quiet || (git commit -am "[automated] Update json files and markdown cache" && git push)
+
+
+      # Create a PR if there are too many lines changed
+      - name: Create PR with changes
+        if: ${{ steps.check_lines.outputs.changes }}
+        uses: peter-evans/create-pull-request@v5
         with:
-          default_author: github_actions
+          token: ${{ secrets.CREATE_PR_TOKEN }}
+          commit-message: 'chore: update pipeline.json and component.json'
+          title: 'chore: update pipeline.json and component.json'
+          body: 'This PR was automatically created by a GitHub Action because there were too many lines changed in the pipeline.json and component.json files.'
+          branch: 'chore/update-pipeline-json-and-component-json'
+          delete-branch: true
+          draft: false

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/nf-co.re'
+      github.repository == 'nf-core/website'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later

.gitignore

@@ -23,3 +23,4 @@ pnpm-debug.log*
 
 # Local Netlify folder
 .netlify
+src/content/pipelines

.pre-commit-config.yaml

@@ -3,8 +3,9 @@ repos:
     rev: 'v2.7.1'
     hooks:
       - id: prettier
-        additional_dependencies: [prettier@2.7.1, prettier-plugin-svelte@^2.10.1, prettier-plugin-astro@^0.10.0]
+        additional_dependencies:
+          - prettier@2.7.1
+          - prettier-plugin-svelte@^2.7.1
+          - prettier-plugin-astro@^0.10.0
         args: [--plugin=prettier-plugin-svelte, --plugin=prettier-plugin-astro]
         files: \.(astro|svelte)$
-
-

.prettierrc.cjs

@@ -2,18 +2,24 @@ module.exports = {
     // TODO: REMOVE SINGLE QUOTES CONFIG LATER
     // Leaving it for now to minimise diffs, but double quote is more consistent with the rest of nf-core
     singleQuote: true,
+    trailingComma: 'all',
     //////
 
     printWidth: 120,
 
-    // pnpm support, for VSCode?
-    plugins: [require.resolve('prettier-plugin-astro')],
+    plugins: [require.resolve('prettier-plugin-astro'), require.resolve('prettier-plugin-svelte')],
     overrides: [
         {
             files: '*.astro',
             options: {
                 parser: 'astro',
             },
         },
+        {
+            files: '*.svelte',
+            options: {
+                parser: 'svelte',
+            },
+        },
     ],
 };

CODE_OF_CONDUCT.md

@@ -1,7 +1,7 @@
 ---
 title: Code of Conduct
 description: The nf-core code of conduct
-md_github_url: https://github.com/nf-core/nf-co.re/blob/main/CODE_OF_CONDUCT.md
+md_github_url: https://github.com/nf-core/website/blob/main/CODE_OF_CONDUCT.md
 ---
 
 # Code of Conduct at nf-core (v1.4)

README.md

@@ -1,7 +1,7 @@
 <img src="public/images/nf-core-logo.svg#gh-light-mode-only" width="400">
 <img src="public/images/nf-core-logo-darkbg.svg#gh-dark-mode-only" width="400">
 
-# [nf-co.re](https://github.com/nf-core/nf-co.re)
+# [nf-co.re](https://github.com/nf-core/website)
 
 This repository contains code for the nf-core website: **<http://nf-co.re/>**
 
@@ -24,8 +24,8 @@ Here's how the website is built:
 To make edits to the website, fork the repository to your own user on GitHub and then clone to your local system.
 
 ```bash
-gh repo fork nf-core/nf-co.re
-cd nf-co.re/
+gh repo fork nf-core/website nf-core_website
+cd nf-core_website/
 ```
 
 ### Installing dependencies
@@ -71,38 +71,11 @@ npm run build-component-json
 npm run build-cache-force
 ```
 
-<!-- ## Production Server Setup
-
-### Deployment
-
-The website is deployed via GitHub Actions ([`.github/workflows/web-deploy.yml`](https://github.com/nf-core/nf-co.re/blob/master/.github/workflows/web-deploy.yml)).
-This script runs PHP composer and npm, then syncs the required files to the web server via FTP. -->
-
 ### Tools API docs
 
 Tools docs are built using GitHub Actions on the nf-core/tools repo using Sphinx.
 [These actions](https://github.com/nf-core/tools/blob/master/.github/workflows/tools-api-docs-release.yml) sync the built HTML files via FTP.
 
-<!-- ### GitHub web hooks
-
-There is a GitHub web hook at the nf-core organisation level which triggers the pipeline update script whenever a repo is created, or has a release etc.
-This pings the `deploy_pipelines.php` script. -->
-
-<!-- ### Stats cronjob
-
-The web server needs the following cronjobs running to scrape statistics and udates:
-
-```cron
-0 0 * * * /usr/local/bin/php /path/to/deployment/update_stats.php >> /home/nfcore/update.log 2>&1
-0 2 * * * /usr/local/bin/php /path/to/deployment/update_issue_stats.php >> /home/nfcore/update.log 2>&1
-0 0 * * 0 /usr/local/bin/php /path/to/deployment/update_fontawesome_icons.php >> /home/nfcore/update.log 2>&
-```
-
-Remember to replace `/path/to/deployment/` with your actual deployment directory.
-
-The `update_issue_stats.php` script can use a lot of GitHub API calls, so should run at least one hour after the `update_stats.php` script last finished.
-This is not because the script takes an hour to run, but because the GitHub API rate-limiting counts the number of calls within an hour. -->
-
 ## Contribution guidelines
 
 If you are looking forward to contribute to the website or add your institution to the official list of contributors, please have a look at the [CONTRIBUTING.md](./.github/CONTRIBUTING.md).
@@ -116,6 +89,6 @@ If you have any questions or issues please send us a message on [Slack](https://
 Phil Ewels ([@ewels](http://github.com/ewels/)) built the initial website, but there have been many contributors to the content and documentation.
 Matthias Hörtenhuber ([@mashehu](https://github.com/mashehu)) worked on the concept and code for the new website rewrite.
 
-See the [repo contributors](https://github.com/nf-core/nf-co.re/graphs/contributors) for more details.
+See the [repo contributors](https://github.com/nf-core/website/graphs/contributors) for more details.
 
 Kudos to the excellent [npm website](https://www.npmjs.com), which provided inspiration for the design of the pipeline pages.

astro.config.mjs

@@ -1,5 +1,6 @@
 import admonitionsPlugin from './bin/remark-admonitions.js';
 import { mermaid } from './bin/remark-mermaid.ts';
+import pipelines_json from '/public/pipelines.json';
 import githubDarkDimmed from '/public/themes/github-dark-dimmed.json';
 import mdx from '@astrojs/mdx';
 import netlify from '@astrojs/netlify/functions';
@@ -24,6 +25,16 @@ import emoji from 'remark-emoji';
 import remarkGfm from 'remark-gfm';
 import remarkMath from 'remark-math';
 
+
+const latestToolsRelease = await fetch('https://api.github.com/repos/nf-core/tools/releases/latest')
+    .then((res) => res.json())
+    .then((json) => json.tag_name);
+let latestPipelineReleases = {};
+
+pipelines_json.remote_workflows.map(
+    (pipeline) => (latestPipelineReleases[pipeline.name] = `/${pipeline.name}/${pipeline.releases[0].tag_name}/`),
+);
+const latestTollsURL = `/tools/docs/'+${latestToolsRelease}`;
 // https://astro.build/config
 export default defineConfig({
     site: 'https://nf-co.re/',
@@ -32,6 +43,10 @@ export default defineConfig({
         assets: true,
     },
     adapter: netlify(),
+    redirects: {
+        [latestTollsURL]: 'https://oldsite.nf-co.re/tools/docs/latest/',
+        ...latestPipelineReleases,
+    },
     integrations: [
         svelte(),
         sitemap(),
@@ -47,6 +62,7 @@ export default defineConfig({
     ],
     build: {
         inlineStylesheets: 'auto',
+        format: 'file',
     },
     vite: {
         plugins: [
@@ -55,6 +71,7 @@ export default defineConfig({
                 // avoid flash of unstyled text by interjecting fallback system fonts https://developer.chrome.com/blog/framework-tools-font-fallback/#using-fontaine-library
                 fallbacks: ['BlinkMacSystemFont', 'Segoe UI', 'Helvetica Neue', 'Arial', 'Noto Sans'],
                 resolvePath: (id) => new URL(`./public${id}`, import.meta.url),
+                skipFontFaceGeneration: (fallbackName) => fallbackName === 'Font Awesome 6 Pro) fallback',
             }),
         ],
         ssr: {

bin/build-cache.js

@@ -46,13 +46,13 @@ export const buildCache = async () => {
             cache.set(cache_key, content);
             // console.log(`Cached ${cache_key}`);
           } else {
-            console.log(`Already cached ${cache_key}`);
+            // console.log(`Already cached ${cache_key}`);
           }
-        })
+        }),
       );
     }
 
-  bar.tick();
+    bar.tick();
   }
   return true;
 };

bin/components.json.js

@@ -6,7 +6,6 @@ import path, { join } from 'path';
 import ProgressBar from 'progress';
 import { parse } from 'yaml';
 
-
 // get current path
 const __dirname = path.resolve();
 
@@ -66,14 +65,14 @@ export const writeComponentsJson = async () => {
         components.modules.push(module);
       }
       bar.tick();
-    })
+    }),
   );
 
   // Fetch subworkflows concurrently
   const subworkflows = tree
     .filter(
       (file) =>
-        file.path.includes('meta.yml') && file.path.includes('subworkflows/') && !file.path.includes('homer/groseq')
+        file.path.includes('meta.yml') && file.path.includes('subworkflows/') && !file.path.includes('homer/groseq'),
     )
     .map((file) => ({
       name: file.path.replace('subworkflows/nf-core/', '').replace('/meta.yml', ''),
@@ -120,7 +119,7 @@ export const writeComponentsJson = async () => {
       }
 
       bar.tick();
-    })
+    }),
   );
 
   // Update pipelines that use modules and subworkflows
@@ -139,7 +138,7 @@ export const writeComponentsJson = async () => {
               components.modules[index].pipelines = [entry];
             }
           }
-        })
+        }),
       );
     }
 
@@ -155,7 +154,7 @@ export const writeComponentsJson = async () => {
               components.subworkflows[index].pipelines = [entry];
             }
           }
-        })
+        }),
       );
     }
   }