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Use cases

Seqera AI CLI is in beta

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

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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
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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
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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:

CommandDescription
/configGenerate a nextflow.config file
/schemaGenerate a Nextflow schema
/debugRun nextflow lint and preview
/debug-last-runDebug the last local run
/debug-last-run-on-seqeraDebug the last Platform run
/migrate-from-wdlConvert WDL to Nextflow
/migrate-from-snakemakeConvert Snakemake to Nextflow
/convert-python-scriptConvert Python script to Nextflow
/convert-r-scriptConvert R script to Nextflow
/convert-jupyter-notebookConvert Jupyter notebook to Nextflow
/write-nf-testWrite 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
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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
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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

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