A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

:rocket: *Seqera Co-Scientist is available for the hackathon!* :rocket:

Hi everyone! :wave: To help you during the hackathon, we've *added credits to the `nf-core_events` organization on Seqera Cloud* and *added all Hackathon participants to it*. That means you can use *Seqera Co-Scientist*, our AI assistant for Nextflow, nf-core and Seqera Platform, at no cost to you.

*What can it help with?*
• Writing and debugging Nextflow code (including strict syntax fixes, configs and `nextflow_schema.json`)
• Finding nf-core modules and showing you how to run them
• Understanding how an existing pipeline is put together
• Building containers with Wave (e.g. _"Create a container with samtools and bwa from bioconda"_)
• Writing nf-tests and fixing failing ones
• Launching and debugging runs on Seqera Platform

:one: *Install the CLI*
You need Node.js 18+ on macOS, Linux or Windows (WSL).
```npm install -g seqera
seqera --version```
_Getting `seqera: command not found`?_ Make sure your npm global bin folder is on your `PATH`.
_Getting permission errors?_ Run `npm install -g seqera --prefix ~/.npm-global`, then `export PATH="$HOME/.npm-global/bin:$PATH"`.

:two: *Log in*
```seqera login```
A browser window opens where you sign in with your Seqera Cloud account. If it doesn't open, copy the URL from your terminal into your browser.

:three: :warning: *Pick the `nf-core_events` org (important!)*
Co-Scientist bills usage to whichever organization you have selected. If you belong to more than one org, make sure `nf-core_events` is the active one, or the hackathon credits won't be used:
```seqera org            # shows your current org
seqera org switch     # choose nf-core_events```
:four: *Start Co-Scientist*
Start it from inside your pipeline's folder so it can see your files:
```cd /path/to/your/pipeline
seqera ai```
*Handy tips*
• `/help`, or just type `/`, to see the built-in commands and skills
• Shift+Tab switches between *build* mode (makes changes) and *plan* mode (read-only analysis and planning)
• `/goal <task>` keeps it working on a longer task, e.g. `/goal add nf-tests for the new module`
• `/status` shows who you're logged in as and which org is active
• `/credits` shows the org's credit balance and your usage
• `seqera ai -c` picks up your last session where you left off
• It asks for your approval before it runs risky commands or changes files outside your working directory

*Some prompts to try*
> _Show me the structure of <http://main.nf|main.nf>_
> _Find nf-core modules for variant calling_
> _Why is my pipeline failing?_
> _Help me write an nf-test for this module_

*Already using Claude Code, Codex or Copilot?* You can add Co-Scientist to them as a skill with `seqera skill install`.

:books: Docs: <https://docs.seqera.io/platform-cloud/seqera-ai/get-started|docs.seqera.io/platform-cloud/seqera-ai/get-started>

Questions or problems? Ask in this thread. Happy hacking! :tada:

You can install (:one:) _without_ npm and node now, if you want:

```curl -fsSL <https://ai-api.seqera.io/install> | bash```

If the org does not appear for you, this means you logged in with an e-mail different from the one you registered for the hackathon. Message me and I can update the e-mail :wink: