Nextflow’s documentation!

Contents:

• Get started
  • Requirements
  • Installation
  • Updates
  • Stable & Edge releases
  • 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
  • Stub
  • Inputs
  • Outputs
  • When
  • Directives
• Channels
  • Channel types
  • Channel factory
  • Channel methods
• Operators
  • branch
  • buffer
  • choice
  • close
  • collate
  • collect
  • collectFile
  • combine
  • concat
  • count
  • countBy
  • cross
  • distinct
  • dump
  • filter
  • first
  • flatMap
  • flatten
  • groupBy
  • groupTuple
  • ifEmpty
  • into
  • join
  • last
  • map
  • max
  • merge
  • min
  • mix
  • multiMap
  • phase
  • print
  • println
  • randomSample
  • reduce
  • separate
  • set
  • splitCsv
  • splitFasta
  • splitFastq
  • splitText
  • spread
  • sum
  • take
  • tap
  • toInteger
  • toList
  • toSortedList
  • transpose
  • unique
  • until
  • view
• Executors
  • AWS Batch
  • Azure Batch
  • Bridge
  • GA4GH TES
  • Google Life Sciences
  • HTCondor
  • Ignite
  • Kubernetes
  • Local
  • LSF
  • Moab
  • NQSII
  • OAR
  • PBS/Torque
  • PBS Pro
  • SGE
  • SLURM
• 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
  • Pipeline parameters
• Containers
  • Charliecloud
  • Docker
  • Podman
  • Shifter
  • Singularity
• Conda environments
  • Prerequisites
  • How it works
  • Best practices
  • Advanced settings
• Amazon Cloud
  • AWS security credentials
  • AWS IAM policies
  • AWS Batch
  • Container Options
  • Custom AMI
  • Jobs & Execution
  • Advanced configuration
• Amazon S3 storage
  • S3 path
  • Security credentials
  • China regions
  • Advanced configuration
• Azure Cloud
  • Requirements
  • Azure Blob Storage
  • Azure File Shares
  • Azure Batch
  • Advanced settings
• Google Cloud
  • Credentials
  • Cloud Batch
  • Cloud Life Sciences
• 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
• Metrics
  • CPU Usage
  • Memory Usage
  • Job Duration
  • I/O Usage
• 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
• Plugins
  • Main concepts
  • Configuration
  • Index
  • Import operators from plugin
  • Import custom functions from plugin
• Secrets
  • How it works
  • Command line
  • Configuration file
  • Process secrets