Merge branch 'main' of github.com:nf-core/website into add-docsearch

# Conflicts:
#	package-lock.json
#	package.json

.github/CONTRIBUTING.md

@@ -5,6 +5,7 @@ menu:
   main:
     weight: 10
 ---
+
 # nf-core/website - Contributing Guidelines
 
 Hi there! Many thanks for taking an interest in improving the nf-core website.

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

@@ -15,6 +15,7 @@ jobs:
       - 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
@@ -34,9 +35,8 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.PIPLINE_JSON_BUILD_TOKEN }}
 
-
       - name: make md cache
-        run: node bin/build-cache.js && tar -cvJf -f .cache.tar.xz .cache
+        run: node bin/build-cache.js && tar -cvJf .cache.tar.xz .cache
         env:
           GITHUB_TOKEN: ${{ secrets.CREATE_CACHE_MD_TOKEN }}
 
@@ -72,23 +72,23 @@ jobs:
       # Commit and push the changes if there are not too many lines changed
       - name: Commit and push changes
         if: ${{ !steps.check_lines.outputs.changes }}
-        uses: EndBug/add-and-commit@v9
-        with:
-          default_author: user_info
-          author_name: nf-core-bot
-          author_email: nf-core-bot@users.noreply.github.com
+        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:
           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"
+          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
-
-

.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',
+            },
+        },
     ],
 };

README.md

@@ -71,7 +71,6 @@ npm run build-component-json
 npm run build-cache-force
 ```
 
-
 ### Tools API docs
 
 Tools docs are built using GitHub Actions on the nf-core/tools repo using Sphinx.

astro.config.mjs

@@ -24,7 +24,6 @@ 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);

bin/build-cache.js

@@ -5,7 +5,6 @@ import { readFileSync } from 'fs';
 import path from 'path';
 import ProgressBar from 'progress';
 
-
 const cache = Cache.default({
   basePath: './.cache',
   ns: 'nf-core',
@@ -49,12 +48,12 @@ export const buildCache = async () => {
           } else {
             // console.log(`Already cached ${cache_key}`);
           }
-        })
+        }),
       );
     }
 
-  bar.tick();
+    bar.tick();
   }
   return true;
 };
-buildCache();
+buildCache();

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];
             }
           }
-        })
+        }),
       );
     }
   }

bin/pipelines.json.js

@@ -5,7 +5,6 @@ import yaml from 'js-yaml';
 import path, { join } from 'path';
 import ProgressBar from 'progress';
 
-
 // get current path
 const __dirname = path.resolve();
 
@@ -46,7 +45,7 @@ export const writePipelinesJson = async () => {
   await fs.writeFile(
     join(__dirname, '/public/pipeline_names.json'),
     JSON.stringify({ pipeline: names }, null, 4),
-    'utf8'
+    'utf8',
   );
 
   // get ignored_topics from ignored_reops.yml
@@ -67,7 +66,7 @@ export const writePipelinesJson = async () => {
           // filter out entries with _url in the key name
           response.data = Object.keys(response.data)
             .filter(
-              (key) => !key.includes('_url') && !['owner', 'permissions', 'license', 'organization'].includes(key)
+              (key) => !key.includes('_url') && !['owner', 'permissions', 'license', 'organization'].includes(key),
             )
             .reduce((obj, key) => {
               obj[key] = response.data[key];
@@ -127,7 +126,7 @@ export const writePipelinesJson = async () => {
           release.has_schema = await getGitHubFile(name, 'nextflow_schema.json', release.tag_name).then((response) => {
             return response ? true : false;
           });
-        })
+        }),
       );
 
       // get last push to dev branch
@@ -187,16 +186,16 @@ export const writePipelinesJson = async () => {
                   ) {
                     return {
                       modules: Object.keys(
-                        modules_json.repos['https://github.com/nf-core/modules.git'].modules['nf-core']
+                        modules_json.repos['https://github.com/nf-core/modules.git'].modules['nf-core'],
                       ),
                       subworkflows: Object.keys(
-                        modules_json.repos['https://github.com/nf-core/modules.git'].subworkflows['nf-core']
+                        modules_json.repos['https://github.com/nf-core/modules.git'].subworkflows['nf-core'],
                       ),
                     };
                   } else {
                     return {
                       modules: Object.keys(
-                        modules_json.repos['https://github.com/nf-core/modules.git'].modules['nf-core']
+                        modules_json.repos['https://github.com/nf-core/modules.git'].modules['nf-core'],
                       ),
                     };
                   }
@@ -209,7 +208,7 @@ export const writePipelinesJson = async () => {
             });
           }
           return { tag_name, published_at, tag_sha, has_schema, doc_files, components };
-        })
+        }),
       );
 
       // Assign new_releases to data.releases
@@ -238,7 +237,7 @@ export const writePipelinesJson = async () => {
         pipelines.remote_workflows.push(data);
       }
       bar.tick();
-    })
+    }),
   );
 
   // sort the pipelines by name

bin/remark-admonitions.js

@@ -2,7 +2,6 @@
 import { h } from 'hastscript';
 import { visit } from 'unist-util-visit';
 
-
 const acceptableAdmonitionTypes = {
   note: {
     title: 'Note',
@@ -77,7 +76,7 @@ export default function admonitionsPlugin() {
         titleData.hProperties = h(
           'span',
           { class: `admonition-title ` },
-          node.attributes.title ? node.attributes.title : boxInfo.title
+          node.attributes.title ? node.attributes.title : boxInfo.title,
         ).properties;
 
         // Creating the icon's column.
@@ -108,4 +107,4 @@ export default function admonitionsPlugin() {
       }
     });
   };
-}
+}