| biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
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| biolockj.api |
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| 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.assembly |
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| 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.diversity |
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| biolockj.module.diy |
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| biolockj.module.getData.sra |
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| biolockj.module.hello_world |
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| 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.
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| 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.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.otu |
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| 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 |
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| biolockj.module.rnaseq |
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| 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.
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