Peter Kruczkiewicz

Scheme creation

1

To help make it more clear what's being changed or added for the scheme creation module, it would be a good idea to have a base branch to merge into...

Command-line arg variable name and SubtypingParams instance variable name synchronization

1

Command-line [arg variable names](https://github.com/phac-nml/biohansel/blob/development/bio_hansel/main.py#L86) should be synchronized with the [`SubtypingParams`](https://github.com/phac-nml/biohansel/blob/development/bio_hansel/subtyping_params.py) so that they can be all checked for and assigned with a couple lines of code, e.g.: ```python for param_key...

WANTED: Salmonella genomes with trustworthy serovar info!

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Hello SISTR users and *in silico* serotypers! Do you have any *Salmonella* genomes with trustworthy serovar info? Would you like SISTR to provide better serovar predictions? You can help by...

> Output a `WARNING` if < 10 representatives in database for a serovar

Add RabbitTClust (v2.2.1)

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This PR adds [RabbitTClust](https://github.com/RabbitBio/RabbitTClust) (v2.2.1). ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

Update VADR to 1.6.3

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Updating VADR to v1.6.3. Changes based on https://github.com/bioconda/bioconda-recipes/pull/44370 ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds...

Variant not detected near end of reference sequence but detected by Bcftools mpileup/call and visually confirmed

11

Hello, I noticed that Clair3 is not calling a variant near the end of a short reference sequence (position 2265 of Influenza A virus PB2 sequence [OP597571.1](https://www.ncbi.nlm.nih.gov/nuccore/OP597571.1); sequence length=2280). Bcftools...

Speeding up predictions

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Hello, Thank you for developing BERTax! It looks like a really great tool for taxonomic classification of sequences that are typically difficult to classify with tools that rely on big...

Port to Python 3 and other changes

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Hello, I was recently trying to use Genotyphi for subtyping *S. Typhi* genomes and encountered some issues integrating the tool with the rest of the tools in a workflow, so...

Downloading an HTML Galaxy output file (in my case, a QUAST HTML output report) with [`HistoriesClient#downloadDataset`](https://github.com/galaxyproject/blend4j/blob/master/src/main/java/com/github/jmchilton/blend4j/galaxy/HistoriesClientImpl.java#L112) results in a binary file with mangled contents, while downloading from `galaxyUrl + downloadUrl`...