Uses of Interface
biolockj.module.BioModule

Packages that use BioModule

Package	Description
biolockj	The root biolockj package contains core classes used by all BioLockJ pipelines.
biolockj.api
biolockj.exception	This package contains Exception subclasses specific to BioLockJ.
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	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.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	This package contains Parser BioModules in the r16s and WGS sub-packages that are paired with a ClassifierModule via 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.rnaseq
biolockj.module.seq	BioModules used to prepare sequence files or update the metadata prior to classification.
biolockj.pipelines
biolockj.util	Static utilities centralize and organize reusable core methods.

Uses of BioModule in biolockj

Methods in biolockj that return BioModule

Modifier and Type	Method and Description
static BioModule	Pipeline.exeModule() Return the BioModule currently being executed

Methods in biolockj that return types with arguments of type BioModule

Modifier and Type	Method and Description
static List<BioModule>	BioModuleFactory.buildPipeline() Build all modules for the pipeline.
static List<BioModule>	Pipeline.getModules() Return a list of BioModules constructed by the BioModuleFactory

Methods in biolockj with parameters of type BioModule

Modifier and Type	Method and Description
static void	Config.checkDependencies(BioModule module)
protected static void	Pipeline.checkOneModulesDependencies(BioModule module)
static boolean	Config.getBoolean(BioModule module, String property) Parse property value (Y or N) to return boolean, if not found, return false;
static Double	Config.getDoubleVal(BioModule module, String property) Parse property for numeric (double) value
static String	Config.getExe(BioModule module, String property) Get exe.* property name.
static String	Config.getExeParams(BioModule module, String property) Call this function to get the parameters configured for this property. Make sure the last character for non-null results is an empty character for use in bash scripts calling the corresponding executable.
static File	Config.getExistingDir(BioModule module, String property) Get a valid File directory or return null
static File	Config.getExistingFile(BioModule module, String property) Get a valid File or return null.
static List<File>	Config.getExistingFileList(BioModule module, String property)
static File	Config.getExistingFileObject(BioModule module, String property) Build File using module and property name.
static Integer	Config.getIntegerProp(BioModule module, String property) Parse property value as integer
static List<String>	Config.getList(BioModule module, String property) Parse comma delimited property value to return list
static String	Config.getModuleFormProp(BioModule module, String property)
static String	Config.getModulePropName(BioModule module, String property) Return property name after substituting the module name as its prefix.
static Integer	Config.getNonNegativeInteger(BioModule module, String property) Parse property as non-negative integer value
static Double	Config.getPositiveDoubleVal(BioModule module, String property) Parse property as positive double value
static Integer	Config.getPositiveInteger(BioModule module, String property) Parse property as positive integer value
protected List<String>	BioModuleFactory.getPostRequisites(BioModule module) This method returns all module post-requisites (including post-requisites of the post-requisites).
protected List<String>	BioModuleFactory.getPreRequisites(BioModule module) This method returns all module prerequisites (including prerequisites of the prerequisites).
static Set<String>	Config.getSet(BioModule module, String property) Parse comma-separated property value to build an unordered Set
static String	Config.getString(BioModule module, String property)
static String	Config.getString(BioModule module, String property, String defaultVal) Get property value as String.
static Set<String>	Config.getTreeSet(BioModule module, String property) Parse comma-separated property value to build an ordered Set
static boolean	Properties.isValidExeProp(BioModule module, String property) Verify that a given exe property has a valid value.
static boolean	Config.requireBoolean(BioModule module, String property) Required to return a valid boolean or
static Double	Config.requireDoubleVal(BioModule module, String property) Requires valid double value
static File	Config.requireExistingDir(BioModule module, String property) Requires valid existing directory.
static List<File>	Config.requireExistingDirs(BioModule module, String property) Requires valid list of file directories
static File	Config.requireExistingFile(BioModule module, String property) Require valid existing file
static Integer	Config.requireInteger(BioModule module, String property) Requires valid integer value
static List<String>	Config.requireList(BioModule module, String property) Require valid list property
static Double	Config.requirePositiveDouble(BioModule module, String property) Require valid positive double value
static Integer	Config.requirePositiveInteger(BioModule module, String property) Require valid positive integer value
static Set<String>	Config.requireSet(BioModule module, String property) Require valid Set value
static String	Config.requireString(BioModule module, String property) Require valid String value
static void	Config.saveModuleProps(BioModule module)
static void	Config.setConfigProperty(String name, Collection<?> data, BioModule module) Sets a property value in the props cache as a list
static void	Config.setConfigProperty(String genericName, String val, BioModule module) Sets a property value in the props cache
static void	Config.setFilePathProperty(String name, String val, BioModule module)

Uses of BioModule in biolockj.api

Subinterfaces of BioModule in biolockj.api

Modifier and Type	Interface and Description
interface	ApiModule

Methods in biolockj.api with parameters of type BioModule

Modifier and Type	Method and Description
static String	BuildDocs.copyFromModuleResource(BioModule module, String name)
static String	BioLockJ_API.propValue(String property, BioModule module)
static String	BioLockJ_API.propValue(String property, String config, BioModule module) Returns the value for that property (first String) If a second argument is given, it is assumed to be the primary config file.

Uses of BioModule in biolockj.exception

Constructors in biolockj.exception with parameters of type BioModule

Constructor and Description
DockerImageException(BioModule module, String image, String msg)
ValidationException(BioModule module) Generate BioModule specific error message.
ValidationExecutionException(BioModule module) Generate BioModule specific error message.

Uses of BioModule in biolockj.module

Subinterfaces of BioModule in biolockj.module

Modifier and Type	Interface and Description
interface	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.
interface	JavaModule Classes that implement this interface are pure Java modules.
interface	OutsidePipelineWriter Implementing modules get to have write permissions outside of the pipeline.
interface	ReadCounter Identifies modules that can report the number of reads per file in the metadata.
interface	ScriptModule Classes that implement this interface are
interface	SeqModule Classes that implement this interface requires sequence files for input.

Classes in biolockj.module that implement BioModule

Modifier and Type	Class and Description
class	BioModuleImpl Superclass for standard BioModules (classifiers, parsers, etc).
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.
class	Stop Stop a pipeline.

Methods in biolockj.module with parameters of type BioModule

Modifier and Type	Method and Description
int	BioModuleImpl.compareTo(BioModule module)
boolean	BioModuleImpl.isValidInputModule(BioModule module) In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.
boolean	SeqModuleImpl.isValidInputModule(BioModule module)
boolean	JavaModuleImpl.isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
boolean	BioModule.isValidInputModule(BioModule previousModule) BioModules getInputFiles() method typically, but not always, return the previousModule output files.

Uses of BioModule in biolockj.module.assembly

Classes in biolockj.module.assembly that implement BioModule

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 BioModule in biolockj.module.classifier

Subinterfaces of BioModule in biolockj.module.classifier

Modifier and Type	Interface and Description
interface	ClassifierModule Classifier BioModules build one or more bash scripts to call the application on sequence files.

Classes in biolockj.module.classifier that implement BioModule

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

Uses of BioModule in biolockj.module.classifier.r16s

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

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 BioModule in biolockj.module.classifier.wgs

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

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 BioModule in biolockj.module.diversity

Classes in biolockj.module.diversity that implement BioModule

Modifier and Type	Class and Description
class	ShannonDiversity

Methods in biolockj.module.diversity with parameters of type BioModule

Modifier and Type	Method and Description
boolean	ShannonDiversity.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.diy

Classes in biolockj.module.diy that implement BioModule

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 BioModule in biolockj.module.getData.sra

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

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

Uses of BioModule in biolockj.module.hello_world

Classes in biolockj.module.hello_world that implement BioModule

Modifier and Type	Class and Description
class	Hello_Friends
class	Hello_World
class	Step1 First set up a mostly-empty class.
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

Methods in biolockj.module.hello_world with parameters of type BioModule

Modifier and Type	Method and Description
boolean	Step4.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.implicit

Classes in biolockj.module.implicit that implement BioModule

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 BioModule in biolockj.module.implicit.parser

Subinterfaces of BioModule in biolockj.module.implicit.parser

Modifier and Type	Interface and Description
interface	ParserModule This interface defines the required methods to parse ClassifierModule output.

Classes in biolockj.module.implicit.parser that implement BioModule

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

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

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

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

Methods in biolockj.module.implicit.parser.r16s with parameters of type BioModule

Modifier and Type	Method and Description
boolean	RdpHierParser.isValidInputModule(BioModule module)

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

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

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.
class	Metaphlan2Parser This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

Methods in biolockj.module.implicit.parser.wgs with parameters of type BioModule

Modifier and Type	Method and Description
boolean	Humann2Parser.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.implicit.qiime

Classes in biolockj.module.implicit.qiime that implement BioModule

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

Methods in biolockj.module.implicit.qiime with parameters of type BioModule

Modifier and Type	Method and Description
boolean	QiimeClassifier.isValidInputModule(BioModule module) If superclass is fed by another QiimeClassifier, it must be a subclass with biom output.
boolean	MergeQiimeOtuTables.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.report

Classes in biolockj.module.report that implement BioModule

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.

Methods in biolockj.module.report with parameters of type BioModule

Modifier and Type	Method and Description
boolean	JsonReport.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.report.humann2

Classes in biolockj.module.report.humann2 that implement BioModule

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.

Methods in biolockj.module.report.humann2 with parameters of type BioModule

Modifier and Type	Method and Description
protected boolean	Humann2CountModule.isHumann2CountModule(BioModule module) Check the module to determine if it generated OTU count files.
boolean	Humann2CountModule.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.report.otu

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

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.

Methods in biolockj.module.report.otu with parameters of type BioModule

Modifier and Type	Method and Description
protected boolean	OtuCountModule.isOtuModule(BioModule module) Check the module to determine if it generated OTU count files.
boolean	OtuCountModule.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.report.r

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

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.

Methods in biolockj.module.report.r with parameters of type BioModule

Modifier and Type	Method and Description
static File	R_Module.getFunctionLib(BioModule module)
static File	R_CalculateStats.getStatsFile(BioModule module, String level, Boolean isParametric, Boolean isAdjusted) Get the stats file for the given fileType and taxonomy level.

Uses of BioModule in biolockj.module.report.taxa

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

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.
class	TaxaCountModule TBD
class	TransformTaxaTables This utility is used to normalize, log-transform or othewise transfrom data that is stored as taxa counts.

Methods in biolockj.module.report.taxa with parameters of type BioModule

Modifier and Type	Method and Description
boolean	TaxaCountModule.isTaxaModule(BioModule module) Check the module output directory for taxonomy table files generated by BioLockJ.
boolean	TaxaCountModule.isValidInputModule(BioModule module)

Uses of BioModule in biolockj.module.rnaseq

Classes in biolockj.module.rnaseq that implement BioModule

Modifier and Type	Class and Description
class	DESeq2
class	EdgeR

Methods in biolockj.module.rnaseq with parameters of type BioModule

Modifier and Type	Method and Description
boolean	EdgeR.isValidInputModule(BioModule module) edgeR should only take raw values.
boolean	DESeq2.isValidInputModule(BioModule module) DESeq should only take raw values.

Uses of BioModule in biolockj.module.seq

Classes in biolockj.module.seq that implement BioModule

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.

Uses of BioModule in biolockj.pipelines

Methods in biolockj.pipelines with parameters of type BioModule

Modifier and Type	Method and Description
static File	PipelineUtil.markStatus(BioModule module, String statusFlag) Set the status of a module using a status flag file.

Uses of BioModule in biolockj.util

Methods in biolockj.util that return BioModule

Modifier and Type	Method and Description
static BioModule	ModuleUtil.createModuleInstance(String className) Construct a BioModule based on its className to add it to the pipeline.
static BioModule	ModuleUtil.getModule(BioModule module, String className, boolean checkAhead) Get a module with given className unless a classifier module is found 1st. Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
static BioModule	ModuleUtil.getNextModule(BioModule module) BioModules are run in the order configured. Return the module configured to run after the given module.
static BioModule	ModuleUtil.getPreviousModule(BioModule module) BioModules are run in the order configured. Return the module configured to run before the given module.

Methods in biolockj.util that return types with arguments of type BioModule

Modifier and Type	Method and Description
protected static List<BioModule>	DownloadUtil.getDownloadModules() Get the modules to download.
static List<BioModule>	ModuleUtil.getModules(BioModule module, Boolean checkAhead) Return pipeline modules after the given module if checkAhead = TRUE Otherwise return pipeline modules before the given module. If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.

Methods in biolockj.util with parameters of type BioModule

Modifier and Type	Method and Description
static List<String>	DockerUtil.buildSpawnDockerContainerFunction(BioModule module, String startedFlag) Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script path parameters.
static void	DockerUtil.checkDependencies(BioModule module)
static void	BashScriptBuilder.checkDependencies(BioModule module)
static void	ValidationUtil.checkDependencies(BioModule module) This method calls the methods that are used by executeTask to get the validation input.
static void	RMetaUtil.classifyReportableMetadata(BioModule module) Classify and verify the R filter and reportable metadata fields listed in the Config file. All metadata fields are reported unless specific fields are listed in: Config."r.reportFields".
static String	ModuleUtil.displayID(BioModule module) Return the module ID as a 2 digit display number (add leading zero if needed).
static String	ModuleUtil.displayName(BioModule module) Return the name of the module (or an alias if it has one).
static String	ModuleUtil.displaySignature(BioModule module)
static Set<String>	RMetaUtil.getBinaryFields(BioModule module) Get the Config."R_internal.binaryFields" fields containing only 2 non-numeric values.
static ClassifierModule	ModuleUtil.getClassifier(BioModule module, boolean checkAhead) Get a classifier module Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
static String	DockerUtil.getDockerImage(BioModule module) Return the name of the Docker image needed for the given module.
static String	SummaryUtil.getInputSummary(BioModule module) Build a summary of the input files for the given module
static Integer	ModuleUtil.getMinSamplesPerWorker(BioModule module) Return the min number of samples that can be processed per worker script.
static BioModule	ModuleUtil.getModule(BioModule module, String className, boolean checkAhead) Get a module with given className unless a classifier module is found 1st. Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
static String	SummaryUtil.getModuleRunTime(BioModule module) Return duration module ran based on modified data of started file, formatted for display (as hours, minutes, seconds).
static List<BioModule>	ModuleUtil.getModules(BioModule module, Boolean checkAhead) Return pipeline modules after the given module if checkAhead = TRUE Otherwise return pipeline modules before the given module. If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.
static BioModule	ModuleUtil.getNextModule(BioModule module) BioModules are run in the order configured. Return the module configured to run after the given module.
static String	MetaUtil.getNullValue(BioModule module) Nulls left as empty cells do not process corrects in R, so a placeholder value must be defined (even if not used).
static Integer	ModuleUtil.getNumMaxWorkers(BioModule module) For uneven batch sizes, some workers will process 1 extra script.
static Integer	ModuleUtil.getNumWorkers(BioModule module) Get the actual number of worker scripts generated for a given module, minimum value = 1.
static String	SummaryUtil.getOutputDirSummary(BioModule module) Return summary of BioModule output directory, with metrics: Number of output files Mean output file size Path of new metadata file if any created
static BioModule	ModuleUtil.getPreviousModule(BioModule module) BioModules are run in the order configured. Return the module configured to run before the given module.
static String	MetaUtil.getSystemMetaCol(BioModule module, String col) Return a system generated metadata column name based on the module status.
static boolean	ModuleUtil.hasExecuted(BioModule module) Return TRUE if module has executed.
static boolean	ModuleUtil.hasScripts(BioModule module) Check a BioModule for scripts to execute.
static boolean	ModuleUtil.isComplete(BioModule module) Return TRUE if module completed successfully.
static boolean	ModuleUtil.isFirstRModule(BioModule module) Test if module is the first R_Module configured in the pipeline.
static boolean	ModuleUtil.isIncomplete(BioModule module) Return TRUE if module started execution but is not complete.
static boolean	DockerUtil.isLocalImage(BioModule module, String image)
static boolean	ModuleUtil.isMetadataModule(BioModule module) Method determines if the given module is a metadata-module (which does not use/modify sequence data.
static boolean	PathwayUtil.isPathwayModule(BioModule module) Check the module to determine if it generated OTU count files.
static boolean	SeqUtil.isSeqModule(BioModule module) Check the module to determine if it generated sequence file output.
static void	ModuleUtil.markComplete(BioModule module) Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully.
static void	ModuleUtil.markStarted(BioModule module) Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully.
static void	SummaryUtil.reportSuccess(BioModule module) After each module completes, this method is called to track the execution summary. If module is null, the pipeline is complete/successful.
static File	ModuleUtil.requireSubDir(BioModule module, String subDirName) Get BioModule subdirectory File object with given name.
protected static void	SummaryUtil.resetModuleSummary(BioModule module) Modules can be forced to reset to incomplete status.
static boolean	ModuleUtil.subDirExists(BioModule module, String subDirName) Return TRUE if BioModule sub-directory exists
static boolean	RMetaUtil.updateRConfig(BioModule module) Get updated R config props
static Boolean	PathwayUtil.useHumann2RawCount(BioModule module) Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.
static void	ValidationUtil.validateModule(BioModule module)
static void	PathwayUtil.verifyConfig(BioModule module) Verify the HumanN2 Config contains at least one of the following reports are enabled: "humann2.disableGeneFamilies" "humann2.disablePathCoverage" "humann2.disableGeneFamilies"
static void	RMetaUtil.verifyMetadataFieldsExist(BioModule module, String prop, Collection<String> fields) This method verifies the fields given exist in the metadata file.

Method parameters in biolockj.util with type arguments of type BioModule

Modifier and Type	Method and Description
protected static File	DownloadUtil.makeRunAllScript(List<BioModule> modules) This script allows a user to run all R scripts together from a single script.
static void	NextflowUtil.startNextflow(List<BioModule> modules) Call this method to build the Nextflow main.nf for the current pipeline.