This repository contains a completed example of converting a simple bash script into a nextflow workflow, made for the 2024 Nextflow vs Snakemake workshop.
The version of the workflow that was written on the day can be found in main.nf.WORKSHOP_VERSION.
Example data has been sourced from the Snakemake tutorial.
Data includes some short reads in fasta format and a portion of the Saccharomyces cerevisiae genome (if you're wondering why mapping statistics are so poor, it's incomplete).
The nextflow.config file is currently set up to use conda.
There is an environment.yml file under assets/.
If you want, you can create a conda environment manually with conda env create -f environment.yml, and delete the config in nextflow.config.
This will actually make the pipeline execute slightly faster than allowing nextflow to manage the conda env for you.
Otherwise, no configuration is provided. The local executor will be used.