All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- The pipeline now supports IonTorrent input data
- Both Single-End and Paired-End input is now supported
- Test suite is entirely containerised within Singularity
- Versions of all used software is conveniently written into a single file
- Assemblies are automatically cleaned up
- AMRFinder has replaced ARIBA
- SKESA de novo assembly added
- Readme contains simple usage instructions and more detailed breakdown of components
- External nextflow-modules are now fully integrated
- Extensive Nextflow code refactoring
- Memory and CPU usage defaults optimised for all modules
- Optimisation of module invocations to reduce overhead
- PRP identifiers updated
- Updated all utilised databases to latest version
- Various publishDir updates
- Resolved multiple BLAST database referencing errors
- Singularity images are now umasked properly
- Minimum recommended RAM expanded to avoid runtime crashes
- Fixed 'failed to publish file' error
- MLST PRP input issues fixed
- Metadata is now properly saved
- Removed legacy modules (notably ARIBA)
- Reduction to only two software requirements; Singularity and Nextflow