Add agent-readiness discovery endpoints for AI agents

.gitignore

@@ -17,6 +17,12 @@ dist/
 # dependencies
 node_modules/
 
+# synced agent skills source checkout
+.cache/
+
+# agent skill files synced at build time from nextflow-io/agent-skills
+public/.well-known/agent-skills/*/
+
 # logs
 npm-debug.log*
 yarn-debug.log*

Makefile

@@ -13,6 +13,8 @@ publish:
 	 --acl public-read \
 	 --exclude "$0"
 
+	bash scripts/set-s3-agent-metadata.sh
+
 invalidate:
 	aws cloudfront create-invalidation --distribution-id E3RPV5P71OW0UF --paths '/*'
 

infra/cloudfront/README.md

@@ -0,0 +1,20 @@
+# CloudFront agent-readiness configuration
+
+Production hosting uses S3 + CloudFront. Apply these after deploying static files.
+
+## Link response headers (RFC 8288)
+
+1. Create a response headers policy from `response-headers-policy.json`, or attach equivalent `Link` headers to the default cache behavior for `/` and `/index.html`.
+2. Alternatively, rely on `scripts/set-s3-agent-metadata.sh` (runs during `make publish`) which sets S3 object metadata on `index.html`.
+
+## Markdown content negotiation
+
+1. Publish the CloudFront Function in `markdown-negotiation.js`.
+2. Associate it with **viewer-request** on the default behavior.
+3. Ensure `index.md` is deployed to S3 (copied from `public/index.md` via the Astro build).
+
+The function rewrites `/` and `/index.html` to `/index.md` when `Accept: text/markdown` is present.
+
+## Netlify previews
+
+PR previews use `public/_headers` for Link headers and `netlify/edge-functions/markdown-negotiate.js` for markdown negotiation.

infra/cloudfront/markdown-negotiation.js

@@ -0,0 +1,18 @@
+// CloudFront Function: serve markdown when Accept: text/markdown is present.
+// Associate with viewer-request on the nextflow.io CloudFront distribution.
+function handler(event) {
+  var request = event.request;
+  var headers = request.headers;
+  var accept = headers.accept ? headers.accept.value : "";
+  var uri = request.uri;
+
+  if (accept.indexOf("text/markdown") === -1) {
+    return request;
+  }
+
+  if (uri === "/" || uri === "/index.html") {
+    request.uri = "/index.md";
+  }
+
+  return request;
+}

infra/cloudfront/response-headers-policy.json

@@ -0,0 +1,23 @@
+{
+  "Comment": "Link response headers for nextflow.io agent discovery (RFC 8288)",
+  "Name": "nextflow-io-agent-discovery-headers",
+  "HeadersConfig": {
+    "HeaderBehavior": "whitelist",
+    "Headers": {
+      "Quantity": 1,
+      "Items": ["Link"]
+    }
+  },
+  "CustomHeadersConfig": {
+    "Quantity": 1,
+    "Items": [
+      {
+        "Header": "Link",
+        "Value": "</.well-known/api-catalog>; rel=\"api-catalog\", </docs.seqera.io/nextflow/>; rel=\"service-doc\", </openapi.json>; rel=\"service-desc\"",
+        "Override": false
+      }
+    ]
+  },
+  "SecurityHeadersConfig": {},
+  "CorsConfig": {}
+}

infra/dns-aid/README.md

@@ -0,0 +1,18 @@
+# DNS for AI Discovery (DNS-AID)
+
+Publish the records in `nextflow.io.zone` under the `_agents` namespace for `nextflow.io`.
+
+## Requirements
+
+1. Add `_index._agents.nextflow.io` and `_a2a._agents.nextflow.io` SVCB records (see zone file).
+2. Enable DNSSEC on the public zone and publish DS records at your domain registrar.
+3. Verify with DNS-over-HTTPS:
+
+```bash
+curl -s 'https://cloudflare-dns.com/dns-query?name=_index._agents.nextflow.io&type=SVCB' \
+  -H 'accept: application/dns-json'
+```
+
+## Production note
+
+DNS-AID records are managed outside this repository (Route 53, Cloudflare DNS, or your registrar). Apply the zone file through your DNS operations workflow after review.

infra/dns-aid/nextflow.io.zone

@@ -0,0 +1,12 @@
+; DNS for AI Discovery (DNS-AID) records for nextflow.io
+; Deploy this zone (or merge these records) with your DNS provider.
+; Sign the zone with DNSSEC and publish DS records at the registrar.
+
+$ORIGIN nextflow.io.
+$TTL 3600
+
+; Index entrypoint — points agents to the site's API catalog
+_index._agents.nextflow.io. IN SVCB 1 nextflow.io. alpn="h3,h2" port=443 mandatory=alpn,port
+
+; Agent-to-agent discovery entrypoint
+_a2a._agents.nextflow.io. IN SVCB 1 nextflow.io. alpn="h3,h2" port=443 mandatory=alpn,port

netlify/edge-functions/markdown-negotiate.js

@@ -0,0 +1,36 @@
+const MARKDOWN_PATHS = {
+  "/": "/index.md",
+  "/index.html": "/index.md",
+};
+
+export default async function handler(request, context) {
+  const accept = request.headers.get("Accept") ?? "";
+  if (!accept.includes("text/markdown")) {
+    return context.next();
+  }
+
+  const url = new URL(request.url);
+  const markdownPath = MARKDOWN_PATHS[url.pathname];
+  if (!markdownPath) {
+    return context.next();
+  }
+
+  const markdownUrl = new URL(markdownPath, url.origin);
+  const markdownResponse = await context.rewrite(markdownUrl.toString());
+  if (!markdownResponse.ok) {
+    return context.next();
+  }
+
+  const body = await markdownResponse.text();
+  const tokenEstimate = Math.ceil(body.length / 4);
+
+  return new Response(body, {
+    status: 200,
+    headers: {
+      "Content-Type": "text/markdown; charset=utf-8",
+      "x-markdown-tokens": String(tokenEstimate),
+      Vary: "Accept",
+      "Cache-Control": "public, max-age=300, must-revalidate",
+    },
+  });
+}

package.json

@@ -6,7 +6,9 @@
     "dev": "astro dev",
     "start": "astro dev",
     "docs": "bash build_docs.sh",
+    "prebuild": "node scripts/generate-agent-skills-index.mjs",
     "build": "astro check && astro build && bash build_docs.sh",
+    "generate:agent-skills-index": "node scripts/generate-agent-skills-index.mjs",
     "preview": "astro preview",
     "astro": "astro"
   },

public/.well-known/agent-skills/index.json

@@ -0,0 +1,30 @@
+{
+  "$schema": "https://schemas.agentskills.io/discovery/0.2.0/schema.json",
+  "source": "https://github.com/nextflow-io/agent-skills",
+  "skills": [
+    {
+      "name": "create-workflow",
+      "type": "skill-md",
+      "description": "INVOKE THIS SKILL IMMEDIATELY when user asks to: write/create/build a Nextflow pipeline or workflow,\ncreate any bioinformatics pipeline (RNA-seq, DNA-seq, variant calling, ChIP-seq, etc.),\nor compose/chain Nextflow modules from the Nextflow Registry. This skill handles all Nextflow workflow creation tasks.",
+      "url": "https://nextflow.io/.well-known/agent-skills/create-workflow/SKILL.md"
+    },
+    {
+      "name": "install-nextflow",
+      "type": "skill-md",
+      "description": "Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow.",
+      "url": "https://nextflow.io/.well-known/agent-skills/install-nextflow/SKILL.md"
+    },
+    {
+      "name": "launch-workflow",
+      "type": "skill-md",
+      "description": "Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Seqera Platform.",
+      "url": "https://nextflow.io/.well-known/agent-skills/launch-workflow/SKILL.md"
+    },
+    {
+      "name": "run-module",
+      "type": "skill-md",
+      "description": "Run Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules.",
+      "url": "https://nextflow.io/.well-known/agent-skills/run-module/SKILL.md"
+    }
+  ]
+}

public/.well-known/api-catalog

@@ -0,0 +1,13 @@
+{
+  "linkset": [
+    {
+      "anchor": "https://nextflow.io/",
+      "service-doc": [
+        {
+          "href": "https://docs.seqera.io/nextflow/",
+          "type": "text/html"
+        }
+      ]
+    }
+  ]
+}

public/.well-known/mcp/server-card.json

@@ -0,0 +1,11 @@
+{
+  "serverInfo": {
+    "name": "nextflow.io",
+    "version": "1.0.0"
+  },
+  "transport": {
+    "type": "webmcp",
+    "pageUrl": "https://nextflow.io/"
+  },
+  "capabilities": ["tools"]
+}

public/_headers

@@ -0,0 +1,26 @@
+/
+  Link: </.well-known/api-catalog>; rel="api-catalog", </docs.seqera.io/nextflow/>; rel="service-doc"
+
+/index.html
+  Link: </.well-known/api-catalog>; rel="api-catalog", </docs.seqera.io/nextflow/>; rel="service-doc"
+
+/.well-known/api-catalog
+  Content-Type: application/linkset+json
+  Cache-Control: public, max-age=300, must-revalidate
+  Access-Control-Allow-Origin: *
+
+
+/.well-known/mcp/server-card.json
+  Content-Type: application/json
+  Cache-Control: public, max-age=300, must-revalidate
+  Access-Control-Allow-Origin: *
+
+/.well-known/agent-skills/index.json
+  Content-Type: application/json
+  Cache-Control: public, max-age=300, must-revalidate
+  Access-Control-Allow-Origin: *
+
+/index.md
+  Content-Type: text/markdown; charset=utf-8
+  Cache-Control: public, max-age=300, must-revalidate
+  Access-Control-Allow-Origin: *

public/index.md

@@ -0,0 +1,56 @@
+# Nextflow
+
+> Reproducible Scientific Workflows at Scale
+
+Nextflow enables scalable, reproducible, and portable scientific workflows for research and production use cases.
+
+## Quick links
+
+- [Documentation](https://docs.seqera.io/nextflow/)
+- [Community forum](https://community.seqera.io/tag/nextflow)
+- [Training](https://training.nextflow.io/latest/)
+- [Examples](/basic-pipeline.html)
+- [VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow)
+- [Seqera AI assistant](https://seqera.io/ask-ai/)
+
+## Features
+
+### Fast prototyping
+
+Nextflow allows you to write a computational pipeline by making it simpler to put together many different tasks. You may reuse your existing scripts and tools without learning a new language.
+
+### Reproducibility
+
+Nextflow supports [Docker](https://www.docker.com/) and [Singularity](https://apptainer.org/) containers, with Git integration for versioned, self-contained pipelines.
+
+### Continuous checkpoints
+
+Intermediate results are automatically tracked so you can resume from the last successful step.
+
+### Portable
+
+Pipelines run on GridEngine, SLURM, LSF, PBS, Kubernetes, AWS, Google Cloud, Azure, and more without code changes.
+
+### Stream oriented
+
+Nextflow extends the Unix pipes model with a fluent DSL for complex stream interactions and functional composition.
+
+### Unified parallelism
+
+Parallelisation is defined by process input and output declarations; applications scale transparently.
+
+## Community resources
+
+- [nf-core](https://nf-co.re/) — curated community pipelines
+- [Seqera Pipelines](https://seqera.io/pipelines/) — browse open-source pipelines
+- [GitHub issues](https://github.com/nextflow-io/nextflow/issues) — report bugs or request features
+
+## Discovery
+
+Machine-readable resources for agents:
+
+- API catalog: `/.well-known/api-catalog`
+- MCP server card: `/.well-known/mcp/server-card.json`
+- Agent skills: `/.well-known/agent-skills/index.json`
+
+Supported by [Seqera](https://seqera.io).

public/robots.txt

@@ -12,5 +12,6 @@ Disallow: /misc/
 Disallow: /logs/
 Disallow: /tests/
 Disallow: /releases/
+Content-Signal: ai-train=no, search=yes, ai-input=yes
 
 Sitemap: https://nextflow.io/sitemap-index.xml

publish.sh

@@ -17,4 +17,6 @@ aws s3 sync --delete output/docs s3://www2.nextflow.io/docs \
  --storage-class STANDARD \
  --acl public-read \
  --exclude "$0" \
- "$@"
+ "$@"
+
+bash "$(dirname "$0")/scripts/set-s3-agent-metadata.sh"