miguelpmachado
commented
4 years ago - Change SPAdes version
- Add SPAdes v3.14.0 and remove v3.10.1
- Incorporate SPAdes --isolate option for estimated coverage >= 100x
- Change MLST QA/QC
- Samples with species known MLST scheme but for which it was not possible to find a scheme will now raise a warning instead of fail
- Add more statistics
- Save total number of reads and bp sequenced
- Change Docker image
- Change base image to perl:5.30-slim-stretch. This allows to use most recent Perl version but keeping an old Linux distribution for old kernels compatibility.
- Install procps to provide free package to access memory usage
- Do a JDK headless installation
- Add any2fasta (mlst dependency)
- Minor changes
- Add Docker image statistics to README
- Minor fixes
- Correct mlst installation
- Check if the mlst novel alleles file exists before cleaning it
- Catch subprocess error when program to run is not installed