Report Package#
Modules in the biolockj.module.report package process ParserModule output, merge the OTU tables with the metadata, and can generate various reports and notifications.
This package contains the following sub-packages:
- module.report.otu contains modules designed to produce or process otu tables.
- module.report.taxa contains modules designed to produce or process taxa tables.
- module.report.r contains modules that use R to generate statistics and/or visualizations.
- module.report.humann2 contains modules designed to produce or process pathway tables.
Email#
#BioModule biolockj.module.report.Email
Description: Notify user pipeline is complete by emailing out the pipeline summary.
Options:
- mail.encryptedPassword
- mail.from
- mail.smtp.auth
- mail.smtp.host
- mail.smtp.port
- mail.smtp.starttls.enable
- mail.to
JsonReport#
#BioModule biolockj.module.report.JsonReport
Description: This module builds a JSON file from the ParserModule output.
Options:
- report.logBase
- report.taxonomyLevels