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.

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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

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JsonReport#

#BioModule biolockj.module.report.JsonReport

Description: This module builds a JSON file from the ParserModule output.

Options:

• report.logBase
• report.taxonomyLevels

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