Nextflow’s documentation!

Contents:

• Get started
  • Requirements
  • Installation
  • Your first script
• Basic concepts
  • Processes and channels
  • Execution abstraction
  • Scripting language
  • Configuration options
• Nextflow scripting
  • Language basics
  • Implicit variables
  • 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
  • PBS Pro
  • Moab
  • NQSII
  • HTCondor
  • Ignite
  • Kubernetes
  • AWS Batch
  • Google Life Sciences
  • GA4GH TES
  • OAR
• Configuration
  • Configuration file
  • Config scopes
  • Config profiles
  • Environment variables
• DSL 2
  • Function
  • Process
  • Workflow
  • Modules
  • Channel forking
  • Pipes
  • DSL2 migration notes
• Command line interface (CLI)
  • Options
  • Commands
• Amazon Cloud
  • AWS credentials
  • Configuration
  • Custom AMI
  • AWS CLI installation
  • Custom job definition
  • Pipeline execution
  • Hybrid workloads
  • Volume mounts
  • Troubleshooting
  • Advanced configuration
• Amazon S3 storage
  • S3 path
  • Security credentials
  • Advanced configuration
• Google Cloud
  • Requirements
  • Cloud Life Sciences
• Conda environments
  • Prerequisites
  • How it works
  • Best practices
  • Advanced settings
• Docker containers
  • Prerequisites
  • How it works
  • Multiple containers
  • Advanced settings
• Shifter Containers
  • Prerequisites
  • Images
  • How it works
  • Multiple Containers
• Singularity containers
  • Prerequisites
  • Images
  • How it works
  • Multiple containers
  • Singularity & Docker Hub
  • Advanced settings
• Podman containers
  • Prerequisites
  • How it works
  • Multiple containers
  • 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 log
  • 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
  • Decoupling metadata
• Mail & Notifications
  • Mail message
  • Mail notification
  • Workflow notification
• Examples
  • Basic pipeline
  • More examples