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Version dev (3c23334bb)

Get started

Overview
Installation
Environment setup
Your first script

Running pipelines

Command line interface
Configuration
Executors
Caching and resuming
Reports

Developing pipelines

Scripts
Working with files
Processes
Processes (typed)
Workflows
Modules
Notifications
Secrets
Sharing pipelines
VS Code integration

Software dependencies

Git
Containers
Conda environments
Spack environments
Wave containers

Compute & storage

Amazon Web Services
Amazon S3
Azure
Google Cloud
Kubernetes
Fusion file system

Plugins

Overview
Using plugins
Developing plugins
Nextflow plugin registry

Language Reference

Feature flags
Syntax
Standard library
Process reference
Channel factories
Operators

Runtime Reference

CLI reference
Configuration options
Environment variables

Updates

Updating Nextflow
Preparing for strict syntax
Migration notes

Contributing

Overview
Workflow Diagram
Configuration scopes
Packages

Tutorials

Getting started with rnaseq-nf
Getting started with data lineage
Migrating to workflow outputs
Migrating to static types
Understanding task resource metrics
Using Nextflow with Flux

Guides

AWS Java SDK v2
Using the Nextflow Gradle plugin
Migrating to the Nextflow plugin registry
Spot Instance failures and retries

Nextflow is developed by:

Nextflow

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Nextflow documentation is migrating

Nextflow documentation is being migrated to docs.seqera.io/nextflow. This site will remain available throughout the migration.

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