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Readme
Co-Scientist CLI
AI-powered assistant for bioinformatics workflows and Seqera Platform.
Get started
Install the Co-Scientist CLI:
npm install -g seqera
See Installation for a comprehensive installation guide.
Log in to your Seqera account:
seqera login
See Authentication for a comprehensive authentication guide.
Start Co-Scientist:
seqera ai
Run your first prompt:
List my recent workflowsSee Use cases for a comprehensive list of use cases.
Use cases
Co-Scientist is an intelligent command-line assistant that helps you build, run, and manage bioinformatics workflows. The following sections describe several common use cases.
Work with Nextflow
Co-Scientist helps you develop, debug, and understand Nextflow pipelines with AI-powered analysis and code generation.
Working with Nextflow
Understand your pipeline structure:
> Show me the structure of main.nf> What processes are defined in this pipeline?Generate a nextflow.config file:
> Generate a nextflow.config for my pipelineDebug your pipeline:
> Why is my pipeline failing?> Run nextflow lint on my pipelineGenerate a schema (nextflow_schema.json) file:
> Generate a nextflow_schema.json for my pipelineConvert scripts to Nextflow:
> Convert my Python script to a Nextflow processBuild containers with Wave
Co-Scientist can create containerized environments using Wave, without requiring you to write Dockerfiles.
Building containers with Wave
Create a container with conda packages:
> Create a container with samtools and bwa from biocondaCreate a container with pip packages:
> Build a container with pandas, numpy, and scikit-learnGet a container for a specific tool:
> I need a container with FastQC version 0.12.1Note: The assistant will generate a Wave container URL that you can use directly in your Nextflow pipelines or pull with Docker.
Customize your session
Customize your session with command-line options.
Customize your session
Start in a specific directory:
seqera ai -w /path/to/projectSet approval mode for local commands:
seqera ai -a fullExit the assistant
End your Co-Scientist session when done.
Exit the assistant
To end your session:
- Type
/exitor/quit - Press
Ctrl+C
Note: Your conversation history is preserved for the session but not stored permanently.
Use slash commands
Co-Scientist includes built-in slash commands for common workflows.
Use slash commands
Type / to see all available commands:
| Command | Description |
|---|---|
/help (or ?) |
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 |
/session |
Show current session ID |
/sessions |
Browse and switch sessions |
/lsp |
Show LSP server status |
/status |
Show system status (includes composer mode) |
/credits |
Show credit balance and usage |
/approval [mode] |
Show or set approval mode (always/default/suggest) |
/update |
Check CLI updates and next steps |
/feedback |
Open feedback form |
/help-community |
Open community help |
/stickers |
Get Seqera stickers |
Work with data
Co-Scientist helps you manage data through Platform data links and access reference datasets.
Working with data
Browse data links:
> List my data links> Show me the contents of my S3 data linkDownload and upload files:
> Generate a download URL for results/final_report.html> Upload my local results to the data linkAccess reference data:
> Find the human reference genome GRCh38> Search for RNA-Seq test dataWork with local files
Co-Scientist can interact with files in your current working directory.
Work with local files
Start the assistant from your project folder:
cd /path/to/your/project
seqera aiThen, ask the assistant to help with local tasks:
> Show me the structure of main.nf> Add a new process to handle quality controlNote: Local file operations are controlled by approval modes. By default, the assistant will ask for your approval before making changes outside your working directory or running potentially dangerous commands.
Work with nf-core modules
Co-Scientist provides access to over 1,000 nf-core modules for common bioinformatics tasks.
Working with nf-core modules
Search for modules:
> Find nf-core modules for sequence alignment> What modules are available for variant calling?Get module details:
> Show me how to use the nf-core/bwa/mem moduleRun a module:
> Run FastQC on my FASTQ filesNote: The assistant can generate the exact Nextflow command with proper parameters for your data.
Work with Seqera Platform
Use Seqera Platform capabilities to run and manage workflows at scale with AI assistance.
Working with Seqera Platform
List your workflows:
> List my recent workflowsLaunch a pipeline:
> Launch the nf-core/rnaseq pipeline with the test profileDebug failed runs:
> Why did my last workflow fail?> Get the logs for the failed task in my last runLearn more
- Installation: Detailed installation instructions
- Authentication: Log in, log out, and session management
- Command approval: Control which commands run automatically
- Use cases: Co-Scientist CLI use cases
- Troubleshooting: Troubleshoot common errors