Cornelius Roemer
Cornelius Roemer
### Current Behavior When running refine on the monkeypox builds `hmpxv1` and `hmpxv1_big` we quite often get a failure with `ERROR: No module named 'ipdb' ` ### Expected behavior No...
### Context It'd be good if `augur translate` could interface with nextalign. We have an `explicit_translation.py` script that does the job, but it'd be nice to integrate into `translate`. The...
### Context Related to #1044, sometimes it seems that export validation can fail despite there not being any obvious problem. Insiders know that `--skip-validation` exists in such situations. But we...
### Current Behavior When making a monkeypox build with custom sequences and spiked metadata, Bryan encountered the following strange export validation error: ``` Validating produced JSON Validating schema of 'results/nebraska_hmpxv1/raw_tree.json'......
I followed the instructions with a simple setup: ``` - name: Setup upterm session uses: lhotari/action-upterm@v1 ``` but when trying to connect using: ``` ssh XhMfjw1FxKdix4uQGdWd:[email protected] ``` I get the...
In today's uploads from RKI, I noticed some Delta sequences with collection date just a week ago that have far too few mutations. It appears that the collection date is...
In order to allow Nextstrain share links to indicate the node that one was on when generating the link, you need some sort of unique id for the branch you're...
When I generate an Usher tree with 5000 samples, finding the uploaded sample on the tree can be quite a challenge. It'd be nice if the link "view tree 1"...
I just uploaded some 40 sequences and got this result. Can't open the link, somewhat strange. Thought I let you know: No console errors.
GISAID exports EPI_ISLs in contracted form including things like `EPI_ISL_14884799-14884801` Usher currently doesn't recognize these. It would be great if you could adapt Usher to recognize these. Here's a sample...