Anatomy of a nextflow process

A brief tutorial on nextflow processes and how to use them in context of RNA-seq.

What is nextflow?

Nextflow is a Domain-Specific Language (DSL) that is developed by the friendly folks at Seqera Labs. It is created specifically to handle common bioinformatics data-sets and data-structures and has many tricks up its sleeve that allows for fast prototyping and deployments on any platform.

To learn more about nextflow, please check out my introductory article on nextflow here.

Nextflow Process:

To help build an understanding for a nextflow processes, let’s first take a look at a template snippet of a nextflow process and break it down step by step.

process < name > {

  [ directives ]
// -----------------------------------------------------------------
  input:
    < process inputs >
// -----------------------------------------------------------------
  output:
    < process outputs >
// -----------------------------------------------------------------
  when:
    < condition >
// -----------------------------------------------------------------
  [script|shell|exec]:
    < user script to be executed >

}

For first timers it can be a lot to digest, but once you get the hang of it, its really simple. In fact writing…