Main change was to fix bug with the "kraken" pipeline where downloading the minikraken database worked the first time, but if you tried running samples a second time, only the first sample would be processed.
Other small changes:
- update to link on installation document (thanks @abissett)
- update to help message and reporting which pipeline is being run
- upload example host index and include as default parameter
- upload MEGARes v3 database bwa index and include as default parameter
Contributors
abissett