Cornelius Roemer

I read through the README and `--help` but couldn't figure out what happens when I _don't_ pass a `--key`. Does it diff everything?

I searched for `tsv-diff` via Google and was led to this page where your tool doesn't actually show up. Maybe add `csv-diff` and `tsv-diff` as a topic to the repo...

Q: Can 2-line spacing around `configfile:` be switched off? Too much whitespace

6

I just applied `snakefmt` to nextstrain/monkeypox. While I love the idea of a snakemake formatter and you've done a great job, the result for our main Snakefile is a bit...

**Context** I found S1 mutations a super useful coloring in the pre-Omicron days. Unfortunately, Omicron has so many S1 mutations now that new S1 mutations are no longer identifiable through...

BUG: Nucleotide and corresponding amino acid mutation occasionally on different branch

3

### Current Behavior It sometimes happens that nt and the corresponding aa mutation are not on the same branch ### Expected behavior Nucleotide and the corresponding amino acid mutations (if...

Being developed in neherlab/ncov-simple in this pr https://github.com/neherlab/ncov-simple/pull/27 May eventually be ported to ncov once ready

BUG: `The target 'col-clade_13_OP205131' could not be identified in the dom, tip: check spelling`

2

I just got this bug and I have no idea what it means! Check spelling of what? This is the link I used: https://master.clades.nextstrain.org/?dataset-name=MPXV&input-fasta=https%3A%2F%2Fmpox-lapis.genspectrum.org%2Fv1%2Fsample%2Ffasta%3ForderBy%3Drandom%26limit%3D200%26country%3DUnited%2BKingdom%26yearFrom%3D2022%26downloadAsFile%3Dtrue I'm running this on Chrome on...

Matthijs Welkers made a good suggestion to make the primer feature more useful. Right now primer mutations are not surfaced in sequence view. We could surface them similar to how...

ENH: Primers should not have to match reference 100%, use mismatch-tolerant alignment

1

Matthijs Welkers mentioned that he had tried to use Nextclade's primer feature with monkeypox (he has published an amplicon tiling scheme for nanopore) but that he got an error when...