Snakemake vs MultiQC reports
MultiQC is very useful in obtaining summary reports of runs. However, snakemake also provides a report as pointed out by @bakma in issue #118 (closed) In that case, all summary figures are created by custom rules, and there is an added benefit of having runtime reports. The question now is: do we want to keep only one of the two, keep the best parts of each to avoid the overhead pf snakemake reports with the figure creation, or have a temporary solution for now and a plan for extension in v1.0.0? This is more pertinent to @zavolan @bakma @kanitz , but if you have insights on use and scenarios, contribute here.