Meet CoScientist¶
Working on the Seqera Platform means moving between the Launchpad, compute environments, datasets, and runs. CoScientist can drive all of that from a conversation, once it is connected to your workspace. In this lesson you open the chat, connect it to your training workspace, and have it inspect and register real Platform assets, so the rest of the course has a working agent to build on.
1. Open the chat and connect to your workspace.¶
Navigate to https://ai.seqera.io/chat and sign in with your Seqera credentials.
Use the Workspace selector in the top navigation to choose the provided training workspace.
2. Confirm the connection and survey the workspace.¶
Writing good prompts
Be specific and state the action or output you want. Working with the agent covers prompting for intent in depth.
Send one prompt to confirm CoScientist can see your workspace and to get a snapshot of what is already in it:
Which Seqera workspace am I connected to? List the compute environments, the pipelines on the Launchpad, and the datasets you can see.
What CoScientist typically does
It names the connected workspace and lists the compute environment(s), Launchpad pipelines, and datasets it can see. The exact wording and the number of items will differ depending on the workspace state.
The same access also covers reference genomes and data links.
Checkpoint
CoScientist correctly names the training workspace and lists at least one compute environment, along with any pipelines and datasets (or reports that none exist yet). If it cannot name the workspace, the connection is not set up; revisit step 1.
3. Ask CoScientist what it can do.¶
Get a baseline picture of the agent's capabilities in this workspace:
What CoScientist typically does
It describes that it can help develop pipelines, launch and monitor runs, browse data, and act on GitHub. The exact wording will differ from run to run.
4. Add rnaseq-nf to the Launchpad.¶
Ask CoScientist to register a pipeline on your behalf:
Add the pipeline https://github.com/nextflow-io/rnaseq-nf to the Launchpad in this workspace, using the available compute environment and a tag to identify it as created by me.
CoScientist will confirm the action or ask which compute environment to use if more than one is available.
Checkpoint
In the Seqera Platform web app, open Launchpad: an entry for rnaseq-nf is now present.
5. Understand what rnaseq-nf does.¶
rnaseq-nf is a small RNA-seq quantification pipeline, a good size to develop and test against.
It builds a Salmon index from a transcriptome (INDEX), runs quality control on the reads (FASTQC), quantifies transcript expression with Salmon (QUANT), and aggregates the results into a single report (MULTIQC).
It ships a small chicken (ggal) test dataset, so a full run finishes in minutes.
graph LR
T[Transcriptome] --> INDEX[INDEX<br/>salmon index]
R[Reads] --> FASTQC[FASTQC<br/>quality control]
R --> QUANT[QUANT<br/>salmon quant]
INDEX --> QUANT
FASTQC --> MULTIQC[MULTIQC<br/>report]
QUANT --> MULTIQC
MULTIQC --> OUT[multiqc_report.html]6. Inspect the compute environment.¶
Ask CoScientist to read the configuration for the compute environment attached to the pipeline:
CoScientist reads the compute-environment configuration and returns the key fields.
Checkpoint
CoScientist reports the compute environment name and platform (for example AWS Batch) matching the training compute environment.
Takeaway¶
You connected CoScientist to your training workspace, had a first conversation, and used it to register and inspect a pipeline. It acts on real Platform assets on your behalf, with your own permissions.
What's next?¶
In the next lesson, learn how to work effectively with the agent before you start changing code.