Skills
This page lists the slash commands and built-in skills available in a Co-Scientist session. To learn how to discover, author, and install skills, see Skills configuration.
Slash commands
Co-Scientist exposes two kinds of slash command in the / palette. TUI commands are handled locally by the CLI to control the session itself:
| Command | Description |
|---|---|
/help | Show available commands |
/exit (/quit, /q) | Exit the application |
/clear | Clear conversation history |
/thinking | Toggle thinking display |
/scroll | Toggle auto-scroll |
/org | Show current organization |
/lsp | Show LSP server status |
/status | Show system status |
/credits | Show credit balance and usage |
/approval | Show or set approval mode |
/feedback | Open feedback form |
/help-community | Open community help |
/stickers | Get Seqera stickers |
The second kind, AI commands, are backed by skills and sent to the AI backend. The built-in ones are listed below, and any skills your deployment exposes appear alongside them in / and /help.
Built-in skills
Your Co-Scientist deployment can expose built-in skills as slash commands. These appear in the / command palette and in /help.
The CLI includes the following built-in skills by default:
| Command | Description |
|---|---|
/nextflow-config | Generate and explain Nextflow configuration files |
/nextflow-schema | Generate nextflow_schema.json and sample sheet schema files |
/debug-local-run | Debug a local Nextflow pipeline run using .nextflow.log, work directories, and related artifacts |
/debug-last-run-on-seqera | Debug the last pipeline run on Seqera Platform |
/convert-jupyter-notebook | Convert Jupyter notebooks to Nextflow pipelines |
/convert-python-script | Convert Python scripts, including standalone scripts and Snakemake-style logic, to Nextflow |
/convert-r-script | Convert R scripts to Nextflow pipelines |
/fix-strict-syntax | Fix Nextflow strict syntax errors and help migrate pipelines to the v2 parser |
/nf-aggregate | Aggregate metrics from Nextflow runs on Seqera Platform using the nf-aggregate pipeline |
/nf-data-lineage | Explore Nextflow data lineage to trace which inputs and processes produced a result |
/nf-pipeline-structure | Analyze a local Nextflow pipeline structure, including processes, workflows, modules, and channel flow |
/nf-run-history | Analyze local Nextflow run history and summarize recent activity, progress, and recurring issues |
/nf-schema-migration | Migrate Nextflow pipelines from nf-validation to nf-schema v2 |
/seqera-mcp | Access Seqera Platform through MCP tools for structured, validated operations |
/seqera-platform-api | Query and manipulate Seqera Platform resources directly through the REST API |
/seqerakit | Write seqerakit YAML configuration for automating Seqera Platform setup |
/simplify | Review changed code for reuse, quality, and efficiency, then clean up issues found |
The exact built-in skills available in your environment may vary by deployment and release. Use /help or type / in the CLI to see the current list.
Payload limits
To keep session payloads small, Co-Scientist caps discovered skill context at 5 KB. The total session payload cap is 20 KB.
Learn more
- Installation: Install, update, and configure the CLI
- Quickstart: Run your first Co-Scientist session
- Authentication: Log in, log out, and manage sessions
- Use cases: Seqera CLI use cases
- Using Co-Scientist: Configure modes, sessions, skills, command approval, and more
- Coding Agents: Install Co-Scientist as a skill in your coding agent
- Troubleshooting: Troubleshoot common errors