-
-
-
-
See what's available
-
- Check out the available pipelines to see if we have what you need. Each comes with release
- details, keywords and a description.
-
-
Available pipelines
-
-
-
-
Run a pipeline
-
- Read the quickstart tutorial to learn how to get set up with the required software and
- tools, and how to launch a nf-core pipeline.
-
-
Quickstart Tutorial
-
-
-
-
Get into the code
-
- If you're interested in contributing to nf-core, take a look at the developer documentation
- to see what's required.
-
-
Developer docs
-
-
+
+
+
+
+
+
See what's available
+
+ Check out the available pipelines to see if we have what you need. Each comes with release
+ details, keywords and a description.
+
+
Available pipelines
+
+
+
+
Run a pipeline
+
+ Read the quickstart tutorial to learn how to get set up with the required software and tools,
+ and how to launch a nf-core pipeline.
+
+
Quickstart Tutorial
+
+
+
+
Get into the code
+
+ If you're interested in contributing to nf-core, take a look at the developer documentation to
+ see what's required.
+
+
Developer docs
+
+
-
+
-
-
+ }
+ svg[data-icon='users'] {
+ margin-bottom: 0.25rem;
+ }
+ svg[data-icon='industry-alt'] {
+ margin-bottom: 0.35rem;
+ }
+ svg[data-icon='laptop-code'] {
+ margin-bottom: 0.55rem;
+ }
+
diff --git a/sites/main-site/src/pages/readmes.astro b/sites/main-site/src/pages/readmes.astro
new file mode 100644
index 0000000000..0f8e71c6ef
--- /dev/null
+++ b/sites/main-site/src/pages/readmes.astro
@@ -0,0 +1,15 @@
+---
+import { getEntry, render, getCollection } from 'astro:content';
+
+import MarkdownTocLayout from '@layouts/MarkdownTocLayout.astro';
+const collection = await getCollection('pipelines');
+// get all id values in collection
+console.log(collection.map((entry) => entry.id));
+
+const entry = await getEntry('pipelines', 'methylseq-2.0.0-README.md');
+const { Content, headings } = await render(entry);
+---
+
+
+
+
diff --git a/sites/main-site/tsconfig.json b/sites/main-site/tsconfig.json
index 5001d538fa..fd01546505 100644
--- a/sites/main-site/tsconfig.json
+++ b/sites/main-site/tsconfig.json
@@ -1,5 +1,6 @@
{
"extends": "astro/tsconfigs/base",
+ "include": [".astro/types.d.ts", "**/*"],
"compilerOptions": {
"baseUrl": ".",
"paths": {
@@ -14,8 +15,5 @@
},
"strictNullChecks": true
},
- "exclude": [
- "node_modules",
- "dist",
- ]
+ "exclude": ["node_modules", "dist"]
}
diff --git a/sites/modules-subworkflows/tsconfig.json b/sites/modules-subworkflows/tsconfig.json
index fbf19aa3dc..3501328ce8 100644
--- a/sites/modules-subworkflows/tsconfig.json
+++ b/sites/modules-subworkflows/tsconfig.json
@@ -1,5 +1,6 @@
{
"extends": "astro/tsconfigs/base",
+ "include": [".astro/types.d.ts", "**/*"],
"compilerOptions": {
"baseUrl": ".",
"paths": {
diff --git a/sites/pipeline-results/astro.config.mjs b/sites/pipeline-results/astro.config.mjs
index 1c995970fd..1bef438f61 100644
--- a/sites/pipeline-results/astro.config.mjs
+++ b/sites/pipeline-results/astro.config.mjs
@@ -34,7 +34,7 @@ pipelines_json.remote_workflows.map(
// https://astro.build/config
export default defineConfig({
site: 'https://nf-co.re/',
- output: 'hybrid',
+ output: 'static',
adapter: netlify(),
prefetch: false,
redirects: {
diff --git a/sites/pipeline-results/src/pages/[pipeline]/[version]/results/[pipeline]/[results_path]/index.astro b/sites/pipeline-results/src/pages/[pipeline]/[version]/results/[pipeline]/[results_path]/index.astro
index 7446e4e160..b9aa38a3e3 100644
--- a/sites/pipeline-results/src/pages/[pipeline]/[version]/results/[pipeline]/[results_path]/index.astro
+++ b/sites/pipeline-results/src/pages/[pipeline]/[version]/results/[pipeline]/[results_path]/index.astro
@@ -16,15 +16,6 @@ export async function getStaticPaths() {
};
}[] = [];
- const prefixes = pipelines_json.remote_workflows
- .map((pipeline) => {
- return pipeline.releases
- .filter((rel) => rel.tag_name !== 'dev')
- .map((release) => {
- return `${pipeline.name}/results-${release.tag_sha}/`;
- });
- })
- .flat();
const awsResponse = await cache
.get('aws.json')
.catch((err) => {
diff --git a/sites/pipeline-results/tsconfig.json b/sites/pipeline-results/tsconfig.json
index 5ac0c74589..3501328ce8 100644
--- a/sites/pipeline-results/tsconfig.json
+++ b/sites/pipeline-results/tsconfig.json
@@ -1,5 +1,6 @@
{
"extends": "astro/tsconfigs/base",
+ "include": [".astro/types.d.ts", "**/*"],
"compilerOptions": {
"baseUrl": ".",
"paths": {
@@ -15,8 +16,5 @@
},
"strictNullChecks": true
},
- "exclude": [
- "node_modules",
- "dist",
- ]
+ "exclude": ["node_modules", "dist"]
}
diff --git a/sites/pipelines/astro.config.mjs b/sites/pipelines/astro.config.mjs
index 287f9bb0e0..9475d9c075 100644
--- a/sites/pipelines/astro.config.mjs
+++ b/sites/pipelines/astro.config.mjs
@@ -32,12 +32,12 @@ let latestPipelineReleases = {};
pipelines_json.remote_workflows.map(
(pipeline) => (latestPipelineReleases[pipeline.name] = `/${pipeline.name}/${pipeline.releases[0].tag_name}/`),
);
-let pipelineResults = {};
-pipelines_json.remote_workflows.map(
- (pipeline) =>
- (pipelineResults[`/${pipeline.name}/:version/results/*`] =
- `https://nf-core-pipeline-results.netlify.app/${pipeline.name}/:version/results/:splat 200!`),
-);
+// let pipelineResults = {};
+// pipelines_json.remote_workflows.map(
+// (pipeline) =>
+// (pipelineResults[`/${pipeline.name}/:version/results/*`] =
+// `https://nf-core-pipeline-results.netlify.app/${pipeline.name}/:version/results/:splat 200!`),
+// );
// https://astro.build/config
export default defineConfig({
site: 'https://nf-co.re/',
@@ -46,7 +46,7 @@ export default defineConfig({
prefetch: false,
redirects: {
...latestPipelineReleases,
- ...pipelineResults,
+ // ...pipelineResults,
},
integrations: [
svelte(),
diff --git a/sites/pipelines/package.json b/sites/pipelines/package.json
index a1c3fb17b0..f98bbaff81 100644
--- a/sites/pipelines/package.json
+++ b/sites/pipelines/package.json
@@ -18,7 +18,8 @@
"test": "playwright test"
},
"dependencies": {
- "@astrojs/mdx": "^3.1.3",
+ "astro": "5.0.0-beta.3",
+ "@astrojs/mdx": "^4.0.0-beta.1",
"@astrojs/netlify": "^5.4.0",
"@iconify-json/fa": "^1.1.8",
"@iconify-json/fa-brands": "^1.1.8",
diff --git a/sites/pipelines/src/content/config.ts b/sites/pipelines/src/content/config.ts
new file mode 100644
index 0000000000..8f57dfa120
--- /dev/null
+++ b/sites/pipelines/src/content/config.ts
@@ -0,0 +1,11 @@
+import { pipelinesLoader } from '@main-site/loaders/pipelines.ts';
+import { defineCollection } from 'astro:content';
+import pipelines_json from '@public/pipelines.json';
+
+const pipeline = defineCollection({
+ loader: pipelinesLoader,
+});
+
+export const collections = {
+ pipeline: pipeline,
+};
diff --git a/sites/pipelines/src/pages/[pipeline]/[version]/docs/[...md_file].astro b/sites/pipelines/src/pages/[pipeline]/[version]/docs/[...md_file].astro
index 05a93aa575..41a61cb38d 100644
--- a/sites/pipelines/src/pages/[pipeline]/[version]/docs/[...md_file].astro
+++ b/sites/pipelines/src/pages/[pipeline]/[version]/docs/[...md_file].astro
@@ -4,7 +4,7 @@ import SidebarToc from '@components/sidebar/SidebarToc.svelte';
import SidebarNav from '@components/sidebar/SidebarNav.astro';
import PipelinePageLayout from '@layouts/PipelinePageLayout.astro';
import pipelines_json from '@public/pipelines.json';
-import { getEntry } from 'astro:content';
+import { getEntry, render } from 'astro:content';
import type { SidebarEntry } from '@utils/types';
import { createLinkOrGroup } from '@utils/functions';
@@ -98,13 +98,9 @@ if (leftSidebar) {
addEntriesToSection(sections, md_files);
}
const version_tag_name = version === 'latest' ? versions[0] : version;
-const cache_key = `${pipeline}/${version_tag_name?.replaceAll('.', '')}/docs/${md_file?.toLowerCase()}`;
-const entry = await getEntry('pipelines', cache_key);
-if (!entry) {
- return Astro.redirect('/404');
-}
-let { Content, headings } = await entry.render();
+const entry = await getEntry('pipeline', `${pipeline}-${version_tag_name}-docs/${md_file}.md`);
+let { Content, headings } = await render(entry);
const max_heading_depth = 2;
// filter out headings that are higher than max_heading_depth
diff --git a/sites/pipelines/src/pages/[pipeline]/[version]/index.astro b/sites/pipelines/src/pages/[pipeline]/[version]/index.astro
index 99c128b7a4..8fd67b0af3 100644
--- a/sites/pipelines/src/pages/[pipeline]/[version]/index.astro
+++ b/sites/pipelines/src/pages/[pipeline]/[version]/index.astro
@@ -1,7 +1,7 @@
---
import PipelinePageLayout from '@layouts/PipelinePageLayout.astro';
import pipelines_json from '@public/pipelines.json';
-import { getEntry } from 'astro:content';
+import { getEntry, render, getCollection } from 'astro:content';
import PipelineSidebar from '@components/pipeline/PipelineSidebar.astro';
export function getStaticPaths() {
var paths: { params: { pipeline: string; version: string }; props: { versions: string[]; md_files; meta } }[] = [];
@@ -33,12 +33,14 @@ let { versions, md_files, meta } = Astro.props;
const description = meta.description;
const is_archived = meta.archived;
const version_tag_name = version === 'latest' ? versions[0] : version;
-const cache_key = `${pipeline}/${version_tag_name.replaceAll('.', '')}/readme`;
-const entry = await getEntry('pipelines', cache_key);
-if (!entry) {
- throw new Error(`No entry found for ${pipeline} ${version}`);
-}
-const { Content, headings } = await entry.render();
+const collection = await getCollection('pipeline');
+console.log(collection.map((entry) => entry.id));
+const entry = await getEntry('pipeline', `${pipeline}-${version_tag_name}-README.md`).catch((e) => {
+ console.error(e);
+ return {};
+});
+
+const { Content, headings } = await render(entry);
const md_github_url = 'https://github.com/nf-core/' + pipeline + '/blob/' + version + '/README.md';
---
diff --git a/sites/pipelines/tsconfig.json b/sites/pipelines/tsconfig.json
index 5ac0c74589..3501328ce8 100644
--- a/sites/pipelines/tsconfig.json
+++ b/sites/pipelines/tsconfig.json
@@ -1,5 +1,6 @@
{
"extends": "astro/tsconfigs/base",
+ "include": [".astro/types.d.ts", "**/*"],
"compilerOptions": {
"baseUrl": ".",
"paths": {
@@ -15,8 +16,5 @@
},
"strictNullChecks": true
},
- "exclude": [
- "node_modules",
- "dist",
- ]
+ "exclude": ["node_modules", "dist"]
}