BioModules#

Some modules are packaged with BioLockJ (see below).

To use modules created by a third-party, add the compiled files (jar file) to your biolockj extentions folder. When you call biolockj, use the --external-modules arg to pass in the location of the extra modules:
biolockj --external-modules </path/to/extentions/folder> <config.properties>

To create your own modules, see Building-Modules.

In all cases, add modules to your BioModule order section to include them in your pipeline.

Built-in BioModules:#

classifiers#

• r16s classifiers
• wgs classifiers

implicit modules#

• implicit parsers
• module.implicit.parser.r16s.md
• module.implicit.parser.wgs.md
• implicit qiime modules

report modules#

• humann2
• report by otu
• report by taxon
• R reports

taxa table modules#

• BuildTaxaTables
• AddPseudoCount
• NormalizeTaxaTables
• NormalizeByReadsPerMillion
• LogTransformTaxaTables
• AddMetadataToTaxaTables

sequence modules#

BioLockJ comes packaged with several modules for sequence pre-processing.

• AwkFastaConverter
• Gunzipper
• KneadData
• Multiplexer
• PearMergeReads
• RarefySeqs
• SeqFileValidator
• TrimPrimers

DIY modules#

• GenMod
• Rmarkdown

List All#

See generated docs for all modules.