README.md

mask-repeats-nf

simple RepeatModeler/Masker pipeline

Introduction

This pipeline soft-masks as many genomes as you want in parallel by running RepeatModeler and then RepeatMasker on them.

Setup

Take a look at our nextflow pipeline advice doc. In general, all you need is to have nextflow installed and configured and it will take care of everything else, including downloading this pipeline. This pipeline runs everything inside of the tetools container.

Running

Just run

nextflow run WarrenLab/mask-repeats-nf --assemblies /path/to/assemblies/*.fa

That's it! It will put all RepeatMasker output in out/.