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 details.

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

snakemake --directory my-analysis --report my-analysis/report.html

This can of course also be used without the --directory option.

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