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An example use of multiQC within snakemake
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README.md

snakemake_multiqc

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.

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