Nextflow
Get started
Basic concepts
Pipeline script
Processes
Channels
Operators
Executors
Configuration
Amazon Cloud
Amazon S3 storage
DNAnexus cloud
Docker containers
Singularity containers
Apache Ignite
Tracing & visualisation
Pipeline sharing
Workflow introspection
Examples
FAQ
Nextflow
Docs
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Nextflow's documentation!
Nextflow's documentation!
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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
NQSII
HTCondor
DRMAA
DNAnexus
Ignite
Kubernetes
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
Singularity containers
Prerequisites
Images
How it works
Multiple 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
Nextflow metadata
Completion handler
Error handler
Notification message
Decoupling metadata
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?