Use cases
Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
Seqera Cloud users receive $20 in free credits to get started with Seqera AI. Contact us for additional credits.
Seqera AI 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
Seqera AI 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:
> /config
Debug your pipeline:
> /debug
> Why is my pipeline failing?
Generate a schema (nextflow_schema.json) file:
> /schema
Convert scripts to Nextflow:
> /convert-python-script
Build containers with Wave
Seqera AI 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 bioconda
Create a container with pip packages:
> Build a container with pandas, numpy, and scikit-learn
Get a container for a specific tool:
> I need a container with FastQC version 0.12.1
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 with an initial query:
seqera ai "list my pipelines"
Continue your last session:
seqera ai -c
Resume a specific session:
seqera ai -s <session-id>
Set approval mode for local commands:
seqera ai --approval-mode full
Exit the assistant
End your Seqera AI session when done.
Exit the assistant
To end your session:
- Type
/exit,/quit, or/q - Press
Ctrl+C
Your conversation history is preserved. You can resume a session later with seqera ai -c to continue your most recent session.
Use slash commands
Seqera AI includes built-in slash commands for common workflows.
TUI commands
These commands are handled locally by the CLI:
| 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 |
AI commands
These commands are sent to the AI backend for processing:
| Command | Description |
|---|---|
/config | Generate a nextflow.config file |
/schema | Generate a Nextflow schema |
/debug | Run nextflow lint and preview |
/debug-last-run | Debug the last local run |
/debug-last-run-on-seqera | Debug the last Platform run |
/migrate-from-wdl | Convert WDL to Nextflow |
/migrate-from-snakemake | Convert Snakemake to Nextflow |
/convert-python-script | Convert Python script to Nextflow |
/convert-r-script | Convert R script to Nextflow |
/convert-jupyter-notebook | Convert Jupyter notebook to Nextflow |
/write-nf-test | Write nf-tests for your pipeline |
Work with data
Seqera AI 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 link
Download and upload files:
> Generate a download URL for results/final_report.html
> Upload my local results to the data link
Access reference data:
> Find the human reference genome GRCh38
> Search for RNA-Seq test data
Work with local files
Seqera AI 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 ai
Then, ask the assistant to help with local tasks:
> Show me the structure of main.nf
> Add a new process to handle quality control
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
Seqera AI 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 module
Run a module:
> Run FastQC on my FASTQ files
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 workflows
Launch a pipeline:
> Launch the nf-core/rnaseq pipeline with the test profile
Debug failed runs:
> Why did my last workflow fail?
> Get the logs for the failed task in my last run
Headless mode
Run Seqera AI in headless mode for scripting and automation. Output is sent to stdout instead of the interactive TUI.
Headless mode
Run a query and pipe the output:
seqera ai --headless "list my pipelines"
Include thinking messages in the output:
seqera ai --headless --show-thinking "debug my pipeline"
Include tool calls in the output:
seqera ai --headless --show-tools "list my workflows"
Headless mode is also auto-detected when stdout is piped (e.g., seqera ai "query" | grep "result").
Session management
Seqera AI preserves your conversation history across sessions. You can resume previous sessions to continue your work.
Session management
Continue your most recent session:
seqera ai -c
Continue with a follow-up question:
seqera ai -c "now run the pipeline with the test profile"
Resume a specific session by ID:
seqera ai -s <session-id>
Learn more
- Seqera AI CLI: Seqera AI CLI overview
- Installation: Detailed installation instructions
- Authentication: Log in, log out, and session management
- Command approval: Control which commands run automatically
- Troubleshooting: Troubleshoot common errors