Pathway Modules

Modules in the biolockj.module.report.humann2 sub-package use ParserModule output to produce and process pathway tables, such as those produced by HumanN2.

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Humann2CountModule

cannot be included in the pipeline run order

Description: Abstract class extends JavaModuleImpl that other humann2 classes extend to inherit shared functionality. Abstract modules cannot be included in the pipeline run order.

Options:

• humann2.disablePathAbundance
• humann2.disablePathCoverage
• humann2.disableGeneFamilies

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AddMetadataToPathwayTables

#BioModule biolockj.module.report.humann2.AddMetadataToPathwayTables

Description: Add metadata columns to the OTU abundance tables.

Options: none

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RemoveLowPathwayCounts

#BioModule biolockj.module.report.humann2.RemoveLowPathwayCounts

Description: This BioModule Pathway counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or genomic contamination.

Options:

• report.minCount

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RemoveScarcePathwayCounts

#BioModule biolockj.module.report.humann2.RemoveScarcePathwayCounts

Description: This BioModule removes scarce pathways not found in enough samples. Each pathway must be found in a configurable percentage of samples to be retained.

Options:

• report.scarceCountCutoff

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