Paul Stodghill
`renameIdxFiles` in `bt2_build.cpp` does not respect `--quiet` Perhaps a `if (verbose)` around the body? ~~~ /opt/bowtie2/bowtie2-build-s version 2.4.5 64-bit Built on 51df6955ec49 Mon Jan 17 00:22:22 UTC 2022 Compiler: gcc...
Recently, we have noticed that whether or not the global average is displayed with user plots depends on the file format of the plot data. In particular, global averages are...
Rfam 14.3 was released in September. Would it be possible to release a new version of Prokka that uses the new models? Alternatively, does someone have a recipe for upgrading...
I have a workflow in which I would like to use, ``` git show tag:foo.md | pandiff - foo.md ``` However, this hangs. Instead what I end up doing is,...
I would like a Markdown output file with Pandoc-style track changes markup instead of CriticMarkup. There doesn't appear to be a combination of command line options that gives this result....
Currently, track changes in DOCX output are tagged as `author="unknown"`. It would be handy if "unknown" could be replaced with a user provided parameter.
This is an enhancement request: Could you parallelize the construction of dotplots (and add a `--threads` argument)? We really appreciate the work that you have done on `trycycler` (and `unicycler`,...
**Describe the bug** When two input genomes have same basename, the genome from the first run is mistakenly used for the second run. The cause is that for the first...