Wolfgang Maier

> > ``` > > * inputs are symlinked with their dataset's extension! > > ``` > > > This can cause problems. As we, unfortunately, have for example this...

@pvanheus just proposed an update (#185) of the ARTIC WF in its dedicated section. I've extended its core part somewhat, but discarded the consensus calling part to highlight the similarity...

@Slugger70 I think by passing a list:paired collection to bwa-mem, you may run into the same blocking WF scheduling issue that you're trying to avoid at the fastp step. At...

Thanks for spotting that MultiQC issue! I'll look into it for EU.

I've updated the EU WF with the Flatten Collection step of the Qualimap output just as you were doing it for AU. Thanks again @Slugger70!

The indexing should be done automatically for you. What's the source of your fasta file? Can you run NormalizeFasta from the Picard package over it?

Ah, I pasted the same result snippet twice above, sorry! The first result should have been: Samples with variants: 334 Total number of variants observed: 1466 Number of sites observed...

... and if I go with the filter `0.95 > float(af) > 0.05` instead of my initial `>=`: Samples with variants: 333 Total number of variants observed: 1452 Number of...

I used plain Python for this: ``` def calc_latest_stats(fun): with open('va_current.tsv') as i: hdr = next(i) samples = set() variants = set() sites = set() for line in i: s,...

The current workflow fails to call indels because it does not use lofreq indelqual to add indel qualities to the mapped reads first. Without those lofreq call skips indels even...