Uses of Class
biolockj.module.BioModuleImpl

Packages that use BioModuleImpl

Package	Description
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.

Uses of BioModuleImpl in biolockj.module

Subclasses of BioModuleImpl in biolockj.module

Modifier and Type	Class and Description
class	JavaModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
class	ScriptModuleImpl Superclass for Java BioModules that will be called in separate instances of the application.
class	SeqModuleImpl Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.

Uses of BioModuleImpl in biolockj.module.classifier

Subclasses of BioModuleImpl in biolockj.module.classifier

Modifier and Type	Class and Description
class	ClassifierModuleImpl This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

Uses of BioModuleImpl in biolockj.module.classifier.r16s

Subclasses of BioModuleImpl in biolockj.module.classifier.r16s

Modifier and Type	Class and Description
class	QiimeClosedRefClassifier This BioModule executes the QIIME script pick_closed_reference_otus.py on a FastA sequence files.
class	QiimeDeNovoClassifier This module runs the QIIME pick_de_novo_otus.py script on FastA sequence files in a single script so it is important to allocate sufficient job resources if running in a clustered environment.
class	QiimeOpenRefClassifier This module runs the QIIME pick_open_reference_otus.py script on FastA sequence files in a single script so it is important to allocate sufficient job resources if running in a clustered environment.
class	RdpClassifier This BioModule uses RDP to assign taxonomy to 16s sequences.

Uses of BioModuleImpl in biolockj.module.classifier.wgs

Subclasses of BioModuleImpl in biolockj.module.classifier.wgs

Modifier and Type	Class and Description
class	Humann2Classifier This BioModule runs biobakery humann2 program to generate the HMP Unified Metabolic Analysis Network HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
class	Kraken2Classifier This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
class	KrakenClassifier This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format.
class	Metaphlan2Classifier This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.

Uses of BioModuleImpl in biolockj.module.implicit

Subclasses of BioModuleImpl in biolockj.module.implicit

Modifier and Type	Class and Description
class	Demultiplexer This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
class	ImportMetadata This BioModule validates the contents/format of the project metadata file and the related Config properties.
class	RegisterNumReads This BioModule parses sequence file to count the number of reads per sample.

Uses of BioModuleImpl in biolockj.module.implicit.parser

Subclasses of BioModuleImpl in biolockj.module.implicit.parser

Modifier and Type	Class and Description
class	ParserModuleImpl Parser BioModules read ClassifierModule output to build standardized OTU count tables.

Uses of BioModuleImpl in biolockj.module.implicit.parser.r16s

Subclasses of BioModuleImpl in biolockj.module.implicit.parser.r16s

Modifier and Type	Class and Description
class	QiimeParser This BioModules parses QiimeClassifier output reports to build standard OTU abundance tables.
class	RdpParser This BioModule parses RDP output files to build standard OTU abundance tables.

Uses of BioModuleImpl in biolockj.module.implicit.parser.wgs

Subclasses of BioModuleImpl in biolockj.module.implicit.parser.wgs

Modifier and Type	Class and Description
class	Humann2Parser This BioModules parses Humann2Classifier output reports to build standard OTU abundance tables. Samples IDs are found in the column headers starting with the 2nd column. The count type depends on the HumanN2 config properties.
class	Kraken2Parser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	KrakenParser This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.
class	Metaphlan2Parser This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

Uses of BioModuleImpl in biolockj.module.implicit.qiime

Subclasses of BioModuleImpl in biolockj.module.implicit.qiime

Modifier and Type	Class and Description
class	BuildQiimeMapping This BioModule converts the metadata file into a tab delimited QIIME mapping file (if provided). The QIIME mapping file is validated by calling QIIME script validate_mapping_file.py
class	MergeQiimeOtuTables This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.
class	QiimeClassifier This BioModule generates the bash script used to create QIIME summary scripts, taxonomy-level reports, and add alpha diversity metrics (if configured) to the metadata file. For a complete list of available metrics, see: http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html

Uses of BioModuleImpl in biolockj.module.report

Subclasses of BioModuleImpl in biolockj.module.report

Modifier and Type	Class and Description
class	Email This BioModule is used to email the user the pipeline execution status and summary.
class	JsonReport This BioModule is used to build a JSON file (summary.json) compiled from all OTUs in the dataset.

Uses of BioModuleImpl in biolockj.module.report.humann2

Subclasses of BioModuleImpl in biolockj.module.report.humann2

Modifier and Type	Class and Description
class	AddMetadataToPathwayTables This BioModule is used to add metadata columns to the HumanN2 pathway abundance, pathway coverage, and gene family tables.
class	Humann2CountModule This abstract superclass is extended by all other modules in this package. Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites.
class	RemoveLowPathwayCounts This BioModule set low Pathway counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or genomic contamination.
class	RemoveScarcePathwayCounts This BioModule removes scarce pathways not found in enough samples. Each pathway must be found in a configurable percentage of samples to be retained.

Uses of BioModuleImpl in biolockj.module.report.otu

Subclasses of BioModuleImpl in biolockj.module.report.otu

Modifier and Type	Class and Description
class	CompileOtuCounts This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.
class	OtuCountModule OtuCount modules reads OTU count assignment tables (1 file/sample) with 2 columns. Col1: Full OTU pathway spanning top to bottom level Col2: Count (# of reads) for the sample.
class	RarefyOtuCounts This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.
class	RemoveLowOtuCounts This BioModule set low OTU counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or contaminents.
class	RemoveScarceOtuCounts This BioModule removes scarce OTUs not found in enough samples. The OTU must be found in a configurable percentage of samples.

Uses of BioModuleImpl in biolockj.module.report.r

Subclasses of BioModuleImpl in biolockj.module.report.r

Modifier and Type	Class and Description
class	R_CalculateStats This BioModule is used to build the R script used to generate taxonomy statistics and plots.
class	R_Module This BioModule is the superclass for R script generating modules.
class	R_PlotEffectSize This BioModule is used to run the R script used to generate OTU-metadata fold-change-barplots for each binary report field.
class	R_PlotMds This BioModule is used to build the R script used to generate MDS plots for each report field and each taxonomy level configured.
class	R_PlotOtus This BioModule is used to build the R script used to generate OTU-metadata box-plots and scatter-plots for each report field and taxonomy level.
class	R_PlotPvalHistograms This BioModule is used to build the R script used to generate p-value histograms for each report field and each taxonomy level configured.

Uses of BioModuleImpl in biolockj.module.report.taxa

Subclasses of BioModuleImpl in biolockj.module.report.taxa

Modifier and Type	Class and Description
class	AddMetadataToTaxaTables This BioModule is used to add metadata columns to the OTU abundance tables.
class	BuildTaxaTables Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.
class	LogTransformTaxaTables This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.
class	NormalizeTaxaTables This utility is used to normalize and/or log-transform the raw OTU counts using the formulas: Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1 Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ] The code implementation supports (log_base = e) and (log_base = 10) which is configured via Constants.REPORT_LOG_BASE property.
class	TaxaCountModule TBD

Uses of BioModuleImpl in biolockj.module.seq

Subclasses of BioModuleImpl in biolockj.module.seq

Modifier and Type	Class and Description
class	AwkFastaConverter This BioModule uses awk and gzip to convert input sequence files into a decompressed fasta file format.
class	Gunzipper This BioModule uses gzip to decompress input sequence files.
class	KneadData This BioModule runs biobakery kneaddata program to remove contaminated DNA. Multiple contaminent DNA databases can be used to filter reads simultaniously. Common contaminents include Human, Viral, and Plasmid DNA.
class	Multiplexer This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an identifying bar-code (if defined in the metatata) is stored in the sequence header. BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.
class	PearMergeReads This BioModule will merge forward and reverse fastq files using PEAR. For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html
class	RarefySeqs This BioModule imposes a minimum and/or maximum number of reads per sample.
class	SeqFileValidator This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
class	TrimPrimers This BioModule removes sequence primers from demultiplexed files. The primers are defined using regular expressions in a separate file.