Uses of Package
biolockj.module

Packages that use biolockj.module

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.module	Pipeline modules are loaded based on the BioModules listed in the Config file. All modules (i.e., implement BioModule) are contained within this package or its sub-packages.
biolockj.module.classifier	This package contains Classifier specific BioModules that build bash scripts to generate taxonomy reports from the sequences files.
biolockj.module.classifier.r16s	This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences. Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule.
biolockj.module.classifier.wgs	This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data. As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to generate standardized OTU abundance tables.
biolockj.module.implicit	The modules in this package are implicitly added to pipelines as needed. These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y.
biolockj.module.implicit.parser	This package contains Parser BioModules in the r16s and WGS sub-packages that are paired with a ClassifierModule via BioModule.getPostRequisiteModules() to run immediately after the classifier.
biolockj.module.implicit.parser.r16s	This package contains Parser BioModules that convert the 16S taxonomy reports generated by 16S classifiers (such as RDP and QIIME) into standardized OTU abundance tables.
biolockj.module.implicit.parser.wgs	This package contains Parser BioModules that convert the WGS taxonomy reports generated by WGS classifiers (such as Kraken, Kraken2 Metaphlan2, or Humann2) into standardized OTU abundance tables.
biolockj.module.implicit.qiime	This package contains BioModules that are implicitly added to QIIME pipeline as needed.
biolockj.module.report	This package contains BioModules that normalize OTU abundance tables output by Parser modules, merges them with the metadata, and generates various reports and notifications.
biolockj.module.report.humann2
biolockj.module.report.otu
biolockj.module.report.r	This package contains BioModules that build pipeline reports from the standard OTU abundance tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files.
biolockj.module.report.taxa
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.
biolockj.util	Static utilities centralize and organize reusable core methods.

Classes in biolockj.module used by biolockj

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
ScriptModule Classes that implement this interface are

Classes in biolockj.module used by biolockj.module

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.

Classes in biolockj.module used by biolockj.module.classifier

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
DatabaseModule Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.
SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Classes in biolockj.module used by biolockj.module.classifier.r16s

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
DatabaseModule Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.
SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Classes in biolockj.module used by biolockj.module.classifier.wgs

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
DatabaseModule Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.
SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Classes in biolockj.module used by biolockj.module.implicit

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.

Classes in biolockj.module used by biolockj.module.implicit.parser

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.implicit.parser.r16s

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.implicit.parser.wgs

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.implicit.qiime

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
DatabaseModule Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.
SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Classes in biolockj.module used by biolockj.module.report

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.report.humann2

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.report.otu

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.report.r

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.report.taxa

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.

Classes in biolockj.module used by biolockj.module.seq

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
DatabaseModule Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.
JavaModule Classes that implement this interface are pure Java modules.
JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
ScriptModule Classes that implement this interface are
ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
SeqModule Classes that implement this interface requires sequence files for input.
SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Classes in biolockj.module used by biolockj.util

Class and Description
BioModule Classes that implement this interface are eligible to be included in a BioLockJ pipeline. Use the #BioModule tag with the class name in the Config file to include a module. The Pipeline class executes BioModules in the order provided in the Config file.
ScriptModule Classes that implement this interface are