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Building with Seqera AI

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CoScientist is Seqera's AI assistant for bioinformatics, integrated directly into the Seqera Platform. It can take on the repetitive parts of pipeline work, from finding modules and wiring processes to launching runs, debugging failures, and writing tests, so you spend less time on plumbing and more on the science. This side quest drives it hands-on against the nextflow-io/rnaseq-nf demo pipeline, taking you from a first conversation through development, debugging, a pull request, a test, and your own reusable agent skill.

Audience & prerequisites

This side quest is designed for learners who have completed the Hello Nextflow course and are comfortable working on the command line with basic Nextflow concepts.

Prerequisites

  • Completed Hello Nextflow or equivalent.
  • Comfortable with the CLI and familiar with basic Nextflow concepts.

Provided sandbox: a training Platform workspace with CoScientist enabled, a working compute environment, and a GitHub account to fork into.

Learning objectives

By the end of this side quest, you will be able to:

  • Converse with CoScientist in the web chat UI to explore and plan pipeline work.
  • Understand how CoScientist takes real actions on the Seqera Platform and GitHub on your behalf.
  • Register a pipeline on the Launchpad and inspect compute and data assets.
  • Work effectively with the agent: prompt for intent, verify what it did, and redirect it when it goes wrong.
  • Fix a failed run from the user side, through launch parameters, without changing code.
  • Fork rnaseq-nf, add a process by reusing an nf-core module, and open a pull request, all from the web chat.
  • Move to the seqera ai CLI to write an nf-test and run it to green.
  • Add a GitHub Actions workflow that runs the tests on every change.
  • Package the nf-test workflow into a reusable CoScientist skill and invoke it as a slash command.

The example pipeline

nextflow-io/rnaseq-nf is a minimal RNA-seq pipeline that runs INDEX and FASTQC in parallel, followed by QUANT (Salmon) and MULTIQC. It ships test data in data/ggal/ and has no nf-test suite yet. That makes it a good target for adding one.

Time estimate: ~3 hours

Get started