Report and Quality Control

MultiQC

Many tools report their output statistics via MultiQC. We store the resulting html file in qc/multiqc.html for each run.

See the Rule Call Graph for an overview of the data flow into MultiQC, and see the multiqc rule for full details.

We also offer to automatically generate a Snakemake report for a run of the pipeline

snakemake --report my-analysis/report.html

This needs to be amended by the --directory option as needed.

For this to work, the Python packages networkx and pygraphviz must be installed:

sudo apt-get install python3-dev graphviz libgraphviz-dev pkg-config python-pip
sudo pip install networkx pygraphviz