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
Co-Scientist includes a set of built-in skills. Invoke a skill directly with its slash command, or describe your task and Co-Scientist loads the matching skill.
note
Built-in skills change from release to release. Treat this page as a guide rather than an inventory. Type / or run /help in your session to see the current list for your deployment.
Build a pipeline
| Command | Description |
|---|---|
/build-nextflow-pipeline | Plan and scaffold a new DSL2 pipeline from scripts, notebooks, papers, or informal instructions, before you write any .nf code |
/create-workflow | Assemble a pipeline from existing modules |
/nf-pipeline-design | Design or refactor pipeline structure, including the shape of main.nf, subworkflow boundaries, and channel and metadata flow |
/nextflow-config | Generate and explain nextflow.config files, including scopes, selectors, profiles, and container runtimes |
/nextflow-schema | Generate nextflow_schema.json and sample sheet schema files |
/triage-pipeline-parameters | Extract each meaningful setting from source material and triage it into a parameter, a pinned constant, or a profile override |
/nextflow-output-patterns | Apply the correct operator idioms when aggregating per-sample outputs, including collectFile, join, groupTuple, and channel-level null handling |
/create-container | Build, claim, or recommend a verified container for a tool, and verify it runs before you write a module |
/nf-docker-scripts | Decide whether custom scripts belong in bin/, in the template directive, or inline |
/search-existing-modules | Search nf-core and the wider community for an existing module before writing your own |
/run-module | Discover, inspect, and run a single module with nextflow module search, view, and run |
Migrate and modernize
| Command | Description |
|---|---|
/convert-jupyter-notebook | Convert Jupyter notebooks to Nextflow processes and workflows |
/convert-python-script | Convert standalone Python scripts to Nextflow |
/convert-r-script | Convert R scripts to Nextflow, with containers and conda environments |
/migrate-from-snakemake | Convert Snakemake workflows to idiomatic DSL2, using a test-first migration loop |
/nextflow-26-syntax | Write, migrate, or debug workflows under the v2 strict-syntax parser used by Nextflow 26+ |
/nf-v2-boolean-params | Fix boolean parameter handling under v2 strict syntax |
/nf-schema-migration | Migrate from nf-validation to nf-schema v2 |
/maintain-nf-core-pipeline | Bring an nf-core pipeline up to date, applying template syncs and module updates before remaining code changes |
/nf-plugin-legacy-migration | Move a legacy plugin to the current plugin registry format |
Test
| Command | Description |
|---|---|
/nf-test | Set up nf-test and write tests for pipelines, modules, and subworkflows |
/repair-nf-test | Diagnose and fix failing nf-tests, snapshot mismatches, and assertion errors |
Debug and repair
| Command | Description |
|---|---|
/debug-local-run | Debug a local run from .nextflow.log, work directories, and task error logs |
/debug-seqera-failed-run | Debug a failed run on Seqera Platform using workflow details, failed tasks, and logs |
/repair-workflow | Fix or improve an existing workflow, with the right validation loop for the problem |
/doctor | Run an end-to-end self-test of your Co-Scientist deployment and report pass/fail per subsystem |
Understand a pipeline or its history
| Command | Description |
|---|---|
/nf-pipeline-structure | Analyze how a local pipeline is organized, including processes, workflows, modules, and data flow |
/nf-run-history | Summarize your recent local runs, including patterns, progress, and recurring issues |
/nextflow-history | Inspect the local Nextflow history and cache, and correlate runs with work directories |
/nf-data-lineage | Trace which inputs and processes produced a result, using the lineage store |
/nf-aggregate | Aggregate metrics across Seqera Platform runs with the nf-aggregate pipeline |
/generate-pipeline-docs | Generate publishable pipeline documentation from the code and its observed run patterns |
/generate-pipeline-memory | Build private notes on a pipeline's run history and failure patterns at your organization |
Work with Seqera Platform
| Command | Description |
|---|---|
/launch-workflow | Launch a pipeline on cloud or high-performance computing (HPC) infrastructure, and choose or confirm a compute environment |
/ce-credentials-setup | Set up compute environments and the cloud or cluster credentials they need |
/seqera-data-links | Add, list, update, and delete data links, including Amazon S3, Google Cloud Storage, and Azure storage |
/seqera-mcp | Access Seqera Platform through Model Context Protocol (MCP) tools for structured, validated operations |
/seqerakit | Write seqerakit YAML to automate Seqera Platform setup |
Choose tools and accelerate
| Command | Description |
|---|---|
/find-alternative-tools | For a given analysis step, find the credible tool options with pros, cons, licensing, and a ranked recommendation |
/enumerate-alternative-tools | Run the same tool enumeration as /find-alternative-tools. The /create-workflow and /nf-pipeline-design planning flows invoke this skill |
/parabricks | Get version-aware guidance on NVIDIA Parabricks pbrun tools and assess GPU readiness |
/genomics-workflow-acceleration | Add optional GPU steps to an existing genomics workflow, with runtime toggles that default to off |
Set up and extend Nextflow
| Command | Description |
|---|---|
/install-nextflow | Install, upgrade, or verify Nextflow and its Java prerequisites |
/nf-plugin-development | Create a plugin from the official template and publish it to the plugin registry |
Review your code
| Command | Description |
|---|---|
/simplify | Review changed code for reuse, quality, and efficiency, then clean up the issues found |
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