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