Inês Mendes

https://github.com/phac-nml/mob-suite

momps, mlst results overwrite when pipeline is resumed

1

Both these components have a a compile_results processes that combines the results and appends them into a single report.tsv file. This file is then symlinked to the publishDir folder. Upon...

Currently, the true_coverage module requires a species to be passed on as an argument, but a scheme is not available for every species. When this happens, the pipeline breaks with...

remove trimmomatic log

1

Due to the very high IO necessary for trimmomatic's log production, some machines will halt this process to a crawl. A fix has been done in PR #178 but I...

Add optional extra params to processes

7

An option to add extra params that we currently do not contemplate in the process is necessary as it will allow users to customise the process. A possible solution is...

When a chewBBACA module is invoked without passing any arguments, the program throws an error and exits with with a code different than zero. Instead, the help for that module...

Obtain specification field data information from JSON schema

1

In the hAMRonizedResult class definition, the field terms for the parsers, and their value types, should be obtained from the schema JSON file and not be hardcoded into the tool....

https://github.com/github/docs/blob/main/CONTRIBUTING.md

- [ ] Improve installation instructions - [ ] Update parsers included - [ ] Add wiki with small tutorial

**Describe the bug** Summarize function failed when no genes were present in the input files. This should be caught and handled by summarize function.