Introduction

This repo is designed to showcase some of the Nextflow bioinformatics work I am undertaking independently.

I am using Nextflow on WSL

Script 1:

Simple initial script that I used to index a target genome with BWA

Genome: https://www.ncbi.nlm.nih.gov/nuccore/CP000325.1/

Script 2:

Pipeline that uses nextflow to download 2 .fastq.gz files and assemble them with SPAdes (genome assembly algorithm)

Two distinct processes - download and assemble

spades.py was installed via conda