Genotype

[lskatz]

What type of PR is this?

• Plugin addition

Describe the change

Added two plugins for genotyping:

• sn_genotype.pl - runs raw genotyping against a database or databases of fasta files
• sn_genotype.escherichia.pl - interprets results from sn_genotype.pl for Escherichia serogrouping

Also fixed emailWhoever.pl to update the email message

• Zip all files as an attachment
• Keep the report.html as an attachment
• Simplify the email body significantly
• Attach SneakerNet.qsub.log and any other files matching *.log to the email

Does it change the usage of SneakerNetPlugins.pl?

No

Did you add any unit testing? Please describe

Removed saveFailedGenomes from testing when run in CI (it's still there normally however)