Uses of Interface
biolockj.module.ScriptModule

Packages that use ScriptModule

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.

Uses of ScriptModule in biolockj

Methods in biolockj with parameters of type ScriptModule

Modifier and Type	Method and Description
protected static boolean	Pipeline.poll(ScriptModule module) The getScriptDir() will contain one main script and one ore more worker scripts. An empty file with appended to the script name is created when execution begins. If successful, an empty file with appended to the script name is created. Upon failure, an empty file with appended to the script name is created. Script status is polled each minute, determining status by counting indicator files. Log outputs the # of started, failed, and successful scripts (if any change). Log repeats the previous message every 10 minutes if no status change is detected.
static void	Processor.submit(ScriptModule module) This method is called by script generating ScriptModules to update the script file-permissions to ensure they are executable by the program.

Uses of ScriptModule in biolockj.module

Subinterfaces of ScriptModule in biolockj.module

Modifier and Type	Interface and Description
interface	JavaModule Classes that implement this interface are pure Java modules.
interface	SeqModule Classes that implement this interface requires sequence files for input.

Classes in biolockj.module that implement ScriptModule

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 ScriptModule in biolockj.module.classifier

Subinterfaces of ScriptModule 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 ScriptModule

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

Uses of ScriptModule in biolockj.module.classifier.r16s

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

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 ScriptModule in biolockj.module.classifier.wgs

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

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 ScriptModule in biolockj.module.implicit

Classes in biolockj.module.implicit that implement ScriptModule

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	RegisterNumReads This BioModule parses sequence file to count the number of reads per sample.

Uses of ScriptModule in biolockj.module.implicit.parser

Subinterfaces of ScriptModule 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 ScriptModule

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

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

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

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 ScriptModule in biolockj.module.implicit.parser.wgs

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

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 ScriptModule in biolockj.module.implicit.qiime

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

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 ScriptModule in biolockj.module.report

Classes in biolockj.module.report that implement ScriptModule

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

Uses of ScriptModule in biolockj.module.report.humann2

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

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 ScriptModule in biolockj.module.report.otu

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

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 ScriptModule in biolockj.module.report.r

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

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 ScriptModule in biolockj.module.report.taxa

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

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 ScriptModule in biolockj.module.seq

Classes in biolockj.module.seq that implement ScriptModule

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 ScriptModule in biolockj.util

Methods in biolockj.util with parameters of type ScriptModule

Modifier and Type	Method and Description
static void	BashScriptBuilder.buildMainScript(ScriptModule module) Build the MIAN script.
static void	BashScriptBuilder.buildScripts(ScriptModule module, List<List<String>> data) This method builds the bash scripts required for the given module. Standard local/cluster pipelines include: 1 MAIN script, 1+ worker-scripts. Docker R_Modules include: 1 MAIN scirpt, 0 worker-scripts - MAIN.R run by MAIN.sh Docker *non-R_Modules* include: 1 MAIN scirpt, 1+ worker-scripts - MAIN.sh runs workers AWS Docker R_Modules include: 0 MAIN scirpts, 0 worker-scripts - MAIN.R run by nextflow AWS Docker *non-R_Modules* include: 0 MAIN scirpts, 1+ worker-scripts MAIN.sh runs workers
protected static String	BashScriptBuilder.getMainScriptExecuteWorkerLine(ScriptModule module, String workerScriptPath, String workerId) Call "execute" on the worker script
static String	SummaryUtil.getScriptDirSummary(ScriptModule module) Return summary of the ScriptModule script directory with metrics: Print main script name Number of worker scripts run Number of worker scripts successful/failed/incomplete Average worker script run time Longest running worker script names/duration Longest running workers script names/duration
protected static String	BashScriptBuilder.getWorkerScriptPath(ScriptModule module, String workerId) Build the file path for the numbered worker script.
protected static List<String>	BashScriptBuilder.initMainScript(ScriptModule module) Create the ScriptModule main script that calls all worker scripts.
protected static List<String>	BashScriptBuilder.initWorkerScript(ScriptModule module, String scriptPath) Create the numbered worker scripts.
static void	LogUtil.syncModuleLogs(ScriptModule module) Not used currently.
protected static void	BashScriptBuilder.verifyConfig(ScriptModule module) If property "pipeline.env" = cluster, require property "cluster.batchCommand", otherwise exit this method.