This is an example pipeline for assembling a genome in nextflow. This pipeline makes use of the software fastp, megahit, and quast.

Installation

To install this pipeline, please make sure you have nextflow installed. This can be accomplished with:

conda create --name nextflow nextflow nf-core nf-test
conda activate nextflow

Now, you can clone this repository:

git clone https://github.com/apetkau/assembly-nf.git
cd assembly-nf

Running

To run the pipeline, please run:

nextflow run main.nf -profile singularity

Output files should be in results/.

You can specify different sets of reads using the --reads parameter.

nextflow run main.nf -profile singularity --reads 'data/reads/*_{1,2}.fastq.gz'

Note the quotes to prevent the shell from expanding the file paths.