Uses of Interface
biolockj.api.ApiModule

Packages that use ApiModule

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.assembly
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
biolockj.module.diy
biolockj.module.getData.sra
biolockj.module.hello_world
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.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
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.rnaseq
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.

Uses of ApiModule in biolockj.module

Classes in biolockj.module that implement ApiModule

Modifier and Type	Class and Description
class	Stop Stop a pipeline.

Uses of ApiModule in biolockj.module.assembly

Classes in biolockj.module.assembly that implement ApiModule

Modifier and Type	Class and Description
class	GenomeAssembly This BioModule builds the bash scripts used to assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and check quality with checkM.

Uses of ApiModule in biolockj.module.classifier.r16s

Classes in biolockj.module.classifier.r16s that implement ApiModule

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 ApiModule in biolockj.module.classifier.wgs

Classes in biolockj.module.classifier.wgs that implement ApiModule

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 ApiModule in biolockj.module.diversity

Classes in biolockj.module.diversity that implement ApiModule

Modifier and Type	Class and Description
class	ShannonDiversity

Uses of ApiModule in biolockj.module.diy

Classes in biolockj.module.diy that implement ApiModule

Modifier and Type	Class and Description
class	ForEachFile
class	ForEachLevel Deprecated.
class	ForEachLoop
class	ForEachSample
class	GenMod This BioModule allows users to call in their own scripts into BLJ
class	Rmarkdown

Uses of ApiModule in biolockj.module.getData.sra

Classes in biolockj.module.getData.sra that implement ApiModule

Modifier and Type	Class and Description
class	SraDownload
class	SraMetaData
class	SraMetaDB
class	SrpSrrConverter

Uses of ApiModule in biolockj.module.hello_world

Classes in biolockj.module.hello_world that implement ApiModule

Modifier and Type	Class and Description
class	Hello_Friends
class	Hello_World
class	Step2 Start with the basic documentation.
class	Step3 Even a very simple module probably uses at least one property.
class	Step4 Specify the acceptable input data type for this module.
class	Step5

Uses of ApiModule in biolockj.module.implicit

Classes in biolockj.module.implicit that implement ApiModule

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.

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

Classes in biolockj.module.implicit.parser.r16s that implement ApiModule

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

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

Classes in biolockj.module.implicit.parser.wgs that implement ApiModule

Modifier and Type	Class and Description
class	Humann2Parser This BioModule 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.

Uses of ApiModule in biolockj.module.report

Classes in biolockj.module.report that implement ApiModule

Modifier and Type	Class and Description
class	Email This BioModule is used to email the user the pipeline execution status and summary.

Uses of ApiModule in biolockj.module.report.otu

Classes in biolockj.module.report.otu that implement ApiModule

Modifier and Type	Class and Description
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.

Uses of ApiModule in biolockj.module.report.r

Classes in biolockj.module.report.r that implement ApiModule

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_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 ApiModule in biolockj.module.report.taxa

Classes in biolockj.module.report.taxa that implement ApiModule

Modifier and Type	Class and Description
class	AddMetadataToTaxaTables This BioModule is used to add metadata columns to the OTU abundance tables.
class	AddPseudoCount
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	NormalizeByReadsPerMillion Normalize each sample for sequencing depth by reporting each value as the number of counts per million counts in a given sample.
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.

Uses of ApiModule in biolockj.module.rnaseq

Classes in biolockj.module.rnaseq that implement ApiModule

Modifier and Type	Class and Description
class	DESeq2
class	EdgeR

Uses of ApiModule in biolockj.module.seq

Classes in biolockj.module.seq that implement ApiModule

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.