Nextflow exercise

This nextflow script performs read cleaning, genome assembly, assembly quality assessment, and bacterial genome characterization of unassembled reads from a bacterial isolate.

Prerequisites:

Create a conda environment with the following tools installed:

conda create -n nextflow_env -y

Activate the conda environment:

conda activate nextflow_env

Installing all the necessary tools:

conda install -c bioconda -c conda-forge skesa fastp mlst quast nextflow -y

Run the nextflow script as following (change the path of reads to your own reads):

nextflow run main_test1.nf --inputR1 ./SRR3215024_1.fastq.gz --inputR2 ./SRR3215024_2.fastq.gz