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Readme

Seqera AI CLI

AI-powered assistant for bioinformatics workflows and Seqera Platform.

Beta: Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.

Note: Seqera Cloud users receive $20 in free credits to get started with Seqera AI. Contact us for additional credits.

Get started

Install the Seqera AI CLI:
```
pip install seqera
```
See Installation for a comprehensive installation guide.
Log in to your Seqera account:
```
seqera login
```
See Authentication for a comprehensive authentication guide.
Start Seqera AI:
```
seqera ai
```
Run your first prompt:
```
/debug
```
See Use cases for a comprehensive list of use cases.

Use cases

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.

Use Seqera AI CLI to debug Nextflow pipeline scripts

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.

Use Seqera AI CLI to build containers with Wave

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

Note: 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/project

Set approval mode for local commands:

seqera ai -a full

Exit the assistant

End your Seqera AI session when done.

Exit the assistant

To end your session:

Type exit or quit
Press Ctrl+C

Note: Your conversation history is preserved for the session but not stored permanently.

Use slash commands

Seqera AI includes built-in slash commands for common workflows.

Use slash commands

Type / to see all available commands:

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

Note: 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

Note: 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.

Use Seqera AI CLI to debug Platform run errors

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

Learn more

Installation: Detailed installation instructions
Authentication: Log in, log out, and session management
Command approval: Control which commands run automatically
Use cases: Seqera AI CLI use cases
Troubleshooting: Troubleshoot common errors