This is a simple, reproducible example runs fastqc, followed by multiqc in a Snakemake workflow using test fastq files from ngs-test-data.
To run the example run the following from a working directory, and make sure to have Snakemake installed on your system either locally or in a snakemake specific conda environment:
git clone --recursive https://github.com/jakevc/snakemake_multiqc.git
cd snakemake_multiqc
snakemake --use-conda
The fastqc and multiqc results will be generated in a data subdirectory.