module.report.humann2
Modules in the biolockj.module.report.humann2 sub-package use ParserModule output to produce and process pathway tables, such as those produced by HumanN2.
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.
- humann2.disablePathAbundance
- humann2.disablePathCoverage
- humann2.disableGeneFamilies
#BioModule biolockj.module.report.humann2.AddMetadataToPathwayTables
Description: Add metadata columns to the OTU abundance tables.
Options: none
#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.
- report.minCount
#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.
- report.scarceCountCutoff
BioLockJ: data-wrangling done right.