module.report

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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