happykhan/nf-mashup

I dunno, something runs mash and makes NJ trees.

Nextflow

nf-mashup

I dunno, something runs mash and makes NJ trees.

runs mash sketch on different fasta files.
runs mash triangle to get pair-wise distances.
runs rapidnj to create NJ tree.

OPTIONAL:

runs mash paste to merge these into a reference database

Installation

To install and set up the pipeline, follow these steps:

Install Nextflow by following the instructions provided in the Nextflow documentation.

Clone the repository:

git clone git@github.com:happykhan/nf-mashup.git

Change into the cloned directory:
```
cd nf-mashup
```
Run the pipeline using Nextflow:
```
nextflow run main.nf
```