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.

---

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

---

AddMetadataToPathwayTables#

#BioModule biolockj.module.report.humann2.AddMetadataToPathwayTables

Description: Add metadata columns to the OTU abundance tables.

Options:

none

---

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

---

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

---