- For each gene in the 'gene screening file', both the 'detection status' (True/False) and the detected allele are written to the IRIDA line-list. Alleles are also reported in the 'gene_detection_status.tsv' output file.
- Limited pipeline parameters to simplify and standardize operation
- Resistance Gene Database is fixed on CARD database.
- Cannot disable post-assembly correction or read trimming.
- Cannot change contig name format
- Cannot provide 'extra spades options' to shovill assembler
- Added thresholds for resistance gene %Coverage and %Identity during secondary screening phase
- The gene screening file used for the analysis is included in the pipeline output
- Fixed issue where sequence data was not being transferred to galaxy
- Initial release of example plugin.