Anton Savchenko

Hi! Maybe I badly misunderstand how Tracer should work, but it seems that many-to-many joint-marginal plot shows axis labels in incorrect, inverse order (or it transposes graphs, to the same...

Hi! When ParGenes reads user-provided files, the last character in the file disappears if not followed by a new line characters. For example, if the last line `msa3.fasta --model partition3.part`...

Hello! When deleting a partition with "-" button in Partitions tab, Tip Dates tab starts to show some unexpected options (see screenshot) regardless if "Use tip dates" enabled or not....

start/end position slippage

4

I may be misunderstanding the output of gnfinder online, but it seems that positions in the Start/End columns sometimes slip. On example below, `Urtica` has start-end coordinates 322-328, but should...

profile -n issue?

1

I noticed that `profile -n` execution log has a line `Excluding intron for the result DNA sequences.` regardless `-n` value. Results after `convert` also seem to be identical. Full commands...

Question: trace back to sequence names

2

Hi! I noticed that individual sequence names do not appear anywhere in output except in temporary files of profile module. Is there an easy way to trace back from UFCG...

Request: output all variants per gene

2

Hi and thanks for the nice resource! Am I right that align module always takes only one variant of multicopy genes? For the sake of, e.g., contamination search, it would...

column names in awk/csv output

1

Question - is it possible to write column names into awk/csv output?

nucleotide easy-search, query bp length issues

3

First of all hi, and thanks for the great tool! I am working on `blastn -task blastn`-like search for barcoding data, and noticed that MMseqs2 changes behavior depending on the...

Error message for invalid config selector incorrectly refers to script as error source

1

## Bug report Wrong error message appears when trying to use breaking `withName: '*'` or `"*"` in a `.config` file. Instead error points to `.nf` file ### Expected behavior Error...