Differences in MultiQC report between BBDUK and minimap2 runs

[hoelzer]

I ran the same command but once with BBDUK. I noticed that the MultiQC reports are quite different. The BBDUK looks nicer in terms of file names and summary statistics.

E.g

while such a plot is missing when using minimap2.

There is this samtools flagstat report instead which is not so nice