Nextflow's documentation!¶

Contents:

Get started
- Requirements
- Installation
- Your first script
Basic concepts
- Processes and channels
- Execution abstraction
- Scripting language
- Configuration options
Pipeline script
- Language basics
- Closures
- Regular expressions
- Files and I/O
Processes
- Script
- Inputs
- Outputs
- When
- Directives
Channels
- Channel types
- Channel factory
- Binding values
- Observing events
Operators
- Filtering operators
- Transforming operators
- Splitting operators
- Combining operators
- Forking operators
- Maths operators
- Other operators
Executors
- Local
- SGE
- LSF
- SLURM
- PBS/Torque
- NQSII
- HTCondor
- Ignite
- Kubernetes
- AWS Batch
- GA4GH TES
Configuration
- Configuration file
- Config scopes
- Config profiles
- Environment variables
Amazon Cloud
- Configuration
- Cluster deployment
- Pipeline execution
- Cluster shutdown
- Cluster auto-scaling
- Spot prices
- Advanced configuration
- AWS Batch
Amazon S3 storage
- S3 path
- Security credentials
- Advanced configuration
Conda environments
- Prerequisites
- How it works
- Best practices
- Advanced settings
Docker containers
- Prerequisites
- How it works
- Multiple containers
- Executable containers
- Advanced settings
Singularity containers
- Prerequisites
- Images
- How it works
- Multiple containers
- Singularity & Docker Hub
- Advanced settings
Apache Ignite
- Cluster daemon
- Pipeline execution
- Execution with MPI
Kubernetes
- Concepts
- Requirements
- Execution
- Interactive login
- Running in a pod
- Pod settings
- Limitation
- Advanced configuration
Tracing & visualisation
- Execution report
- Trace report
- Timeline report
- DAG visualisation
- Weblog via HTTP
Pipeline sharing
- How it works
- Running a pipeline
- Handling revisions
- Commands to manage projects
- SCM configuration file
- Private server configuration
- Local repository configuration
- Publishing your pipeline
- Manage dependencies
Workflow introspection
- Runtime metadata
- Nextflow metadata
- Completion handler
- Error handler
- Notification message
- Decoupling metadata
Mail & Notifications
- Mail message
- Mail notification
- Workflow notification
Examples
- Basic pipeline
- More examples
FAQ
- How do I process multiple input files in parallel?
- How do I get a unique ID based on the file name?
- How do I use the same channel multiple times?
- How do I invoke custom scripts and tools?
- How do I iterate over a process n times?
- How do I iterate over nth files from within a process?
- How do I use a specific version of Nextflow?