nextflow-boilerplate

Boilerplate code for Nextflow pipelines

Installation

Clone this repository

git clone https://github.com/stevekm/nextflow-boilerplate.git
cd nextflow-boilerplate

Install Nextflow in the local directory

make install

(Optional) Test that it worked

make test

Contents

• main.nf: main Nextflow pipeline file

• nextflow.config: Nextflow configuration file

• bin: directory for scripts to use inside the Nextflow pipeline; its contents will be prepended to your PATH when pipeline tasks are executed

• Makefile: shortcuts to common pipeline actions

Software Requirements

• Java 8 (Nextflow)

• GraphViz Dot (to compile flowchart)

• any other requirements needed by your pipeline tasks