Aaron Petkau

Add support for additional PointFinder organisms

1

Only *salmonella* is supported from the PointFinder database. Add support for all other organisms - https://bitbucket.org/genomicepidemiology/pointfinder_db/src * [x] campylobacter * [ ] e.coli * [ ] gonorrhoeae * [ ]...

There is a request for an option to skip running MLST. Something along the lines of `--skip-mlst`.

Set the --pointfinder-organism based on results of organism id instead of relying on the user to provide this information on the command-line.

Add support for multiple types of biological data files

1

It would be nice if `staramr` could support multiple types of input files (such as Genbank) and also compressed versions of each of this files (e.g., gzipped fasta). As an...

# Issue When running staramr where some plasmidfinder incompatibility factors are detected causes staramr to crash with the following message: ``` 2022-10-24 11:47:20 ERROR: Index length not within range, for...

rename haiti group in OrthoMCL lab to be more descriptive of type of data it contains.

Allow setting metadata for NCBI upload in batch format

1

## Describe your idea for a new feature It is currently difficult to fill in the necessary information for exporting samples to NCBI. In particular, the NCBI BioSample identifier must...

Missing ILLUMINAMISEQ constant prevents viewing NCBI Export page

1

## Describe the bug On one of our IRIDA instances, when I go to **Admin > NCBI Exports**, the page fails to load and the following line is found in...

## What needs changed? The version and mechanism of launching Galaxy (using Docker) for integration tests. ## How does it work now? This uses a custom modified version of Galaxy...

## Describe your idea for a new feature Add an option to select all **Associated projects** to display in a project rather than having to select each one individually. Right...