In #182 a --test argument has been added to support testing with GitHub actions. To facilitate quick execution synthetic paired end sequencing data has been created from chatgpt.
Unfortunately, several modules does not work due to different issues - We need to fix / handle the following:
[] Shovill overpolishes the synthetic data, leading to no assembly
[] Meningotype dependency has hardcoded CPU support, leading to later MAC being unsupported
[] Resfinder, Pointfinder, and Disinfinder not supported due to unknown issue with synthetic data
[] CDiff tools like snp_identifier and deletion_identifier not working due to bcftool installation issue (pending on bioconda repo)
[] Seqsero2 Issue on Mac
In #182 a
--testargument has been added to support testing with GitHub actions. To facilitate quick execution synthetic paired end sequencing data has been created from chatgpt.Unfortunately, several modules does not work due to different issues - We need to fix / handle the following:
[] Shovill overpolishes the synthetic data, leading to no assembly
[] Meningotype dependency has hardcoded CPU support, leading to later MAC being unsupported
[] Resfinder, Pointfinder, and Disinfinder not supported due to unknown issue with synthetic data
[] CDiff tools like snp_identifier and deletion_identifier not working due to bcftool installation issue (pending on bioconda repo)
[] Seqsero2 Issue on Mac