Basic concepts

Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data.

It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.

Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.

Processes and channels

In practice a Nextflow pipeline script is made by joining together many different processes. Each process can be written in any scripting language that can be executed by the Linux platform (Bash, Perl, Ruby, Python, etc.).

Processes are executed independently and are isolated from each other, i.e. they do not share a common (writable) state. The only way they can communicate is via asynchronous FIFO queues, called channels in the Nextflow lingo.

Any process can define one or more channels as input and output. The interaction between these processes, and ultimately the pipeline execution flow itself, is implicitly defined by these input and output declarations.

A Nextflow script looks like this:

params.query = "$HOME/sample.fa"
params.db = "$HOME/tools/blast-db/pdb/pdb"

db = file(params.db)
query = file(params.query)

process blastSearch {
    input:
    file query

    output:
    file top_hits

    """
    blastp -db $db -query $query -outfmt 6 > blast_result
    cat blast_result | head -n 10 | cut -f 2 > top_hits
    """
}


process extractTopHits {
    input:
    file top_hits

    output:
    file sequences

    """
    blastdbcmd -db ${db} -entry_batch $top_hits > sequences
    """
}

The above example defines two processes. Their execution order is not determined by the fact that the blastSearch process comes before the extractTopHits in the script (it could also be written the other way around), but because the first defines the channel top_hits in its output declarations while the extractTopHits process defines the same channel in its input declaration, thus establishing a communication link from the blastSearch task towards the extractTopHits task.

Read the Channel and Process sections to learn more about these features.

Execution abstraction

While a process defines what command or script has to be executed, the executor determines how that script is actually run on the target system.

If not otherwise specified, processes are executed on the local computer. The local executor is very useful for pipeline development and test purposes, but for real world computational pipelines an HPC or cloud platform is required.

In other words, Nextflow provides an abstraction between the pipeline’s functional logic and the underlying execution system. Thus it is possible to write a pipeline once and to seamlessly run it on your computer, a grid platform, or the cloud, without modifying it, by simply defining the target execution platform in the configuration file.

The following HPC and cloud platforms are supported:

• Open grid engine
• Univa grid engine
• Platform LSF
• Linux SLURM
• PBS Works
• Torque
• HTCondor

Read the Executors section to learn more about Nextflow executors.

Scripting language

Although Nextflow is designed to be used with a minimal learning curve, without having to study a new programming language and using your current skills, it also provides a powerful scripting DSL.

Nextflow scripting is an extension of the Groovy programming language, which in turn is a super-set of the Java programming language. Thus if you have some knowledge of these languages, or even just some confidence with the C/C++ syntax, you will be comfortable using it.

Read the Pipeline script section to learn about the Nextflow scripting language.

Configuration options

Pipeline configuration properties are defined in a file named nextflow.config in the pipeline execution directory.

This file can be used to define which executor to use, the process’s environment variables, pipeline parameters etc.

A basic configuration file might look like this:

process {
  executor='sge'
  queue = 'cn-el6'
}

env {
  PATH="$PWD/bowtie2:$PWD/tophat2:$PATH"
}

Read the Configuration section to learn more about the Nextflow configuration file and settings.