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 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
  • HTCondor
  • DRMAA
  • DNAnexus
  • Ignite
• 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
• Amazon S3 storage
  • S3 path
  • Security credentials
  • Advanced configuration
• DNAnexus cloud
  • Prerequisites
  • App packing
  • Execution
  • How it works
• Docker containers
  • Prerequisites
  • How it works
  • Multiple containers
  • Executable containers
  • Advanced settings
• Apache Ignite
  • Cluster daemon
  • Pipeline execution
  • Execution with MPI
• Tracing & visualisation
  • Execution report
  • Timeline report
  • DAG visualisation
  • Extrae integration
• Pipeline sharing
  • How it works
  • Running a pipeline
  • Handling revisions
  • Commands to manage projects
  • SCM configuration file
  • Private server configuration
  • Publishing your pipeline
  • Manage dependencies
• Workflow introspection
  • Runtime metadata
  • Completion handler
  • Error handler
  • Notification message
  • Decoupling metadata
• Examples
  • Basic pipeline