biolockj.module

Interface ScriptModule

All Superinterfaces:

BioModule

All Known Subinterfaces:

ClassifierModule, JavaModule, ParserModule, SeqModule

All Known Implementing Classes:

AddMetadataToPathwayTables, AddMetadataToTaxaTables, AddPseudoCount, AwkFastaConverter, BuildQiimeMapping, BuildTaxaTables, ClassifierModuleImpl, CompileOtuCounts, Demultiplexer, DESeq2, EdgeR, ForEachFile, ForEachLevel, ForEachLoop, ForEachSample, GenMod, GenomeAssembly, Gunzipper, Hello_Friends, Hello_World, Humann2Classifier, Humann2CountModule, Humann2Parser, JavaModuleImpl, JsonReport, KneadData, Kraken2Classifier, Kraken2Parser, KrakenClassifier, KrakenParser, LogTransformTaxaTables, MergeQiimeOtuTables, Metaphlan2Classifier, Metaphlan2Parser, Multiplexer, NormalizeByReadsPerMillion, NormalizeTaxaTables, OtuCountModule, ParserModuleImpl, PearMergeReads, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, QiimeParser, R_CalculateStats, R_Module, R_PlotEffectSize, R_PlotMds, R_PlotOtus, R_PlotPvalHistograms, RarefyOtuCounts, RarefySeqs, RdpClassifier, RdpHierParser, RdpParser, RegisterNumReads, RemoveLowOtuCounts, RemoveLowPathwayCounts, RemoveScarceOtuCounts, RemoveScarcePathwayCounts, Rmarkdown, ScriptModuleImpl, SeqFileValidator, SeqModuleImpl, SequenceReadArchive, ShannonDiversity, SraDownload, SraMetaData, SraMetaDB, SrpSrrConverter, Step1, Step2, Step3, Step4, Step5, TaxaCountModule, TransformTaxaTables, TrimPrimers

public interface ScriptModule
extends BioModule

Classes that implement this interface are

Field Summary

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Method returns a nested list of bash script lines to classify samples containing forward reads only.
List<List<String>>	buildScriptForPairedReads(List<File> files) Method returns a nested list of bash script lines to classify samples containing paired reads. The inner list contains the bash script lines required to classify 1 sample.
String[]	getJobParams() Many ScriptModules generate bash or R scripts for the Operating System to run as a Processor. The Processor creates a Process using the parameters supplied by this method and executed in the Runtime environment. Parameters typically contain the full script path and script parameters, if needed.
File	getMainScript() Method returns MAIN module script that calls each of the worker scripts.
File	getScriptDir() ScriptModules that generate scripts to complete their task, create script files in this directory. The main script must begin with prefix and there must only be one main script. The main script executes, or submits to the job queue, each of the other scripts in this directory. The # subscripts generated by the ScriptModule depends upon .
List<String>	getScriptErrors() Return a list of the error messages saved the failure scripts in the module script directory.
Integer	getTimeout() ScriptModule that run scripts can opt to set a timeout (such as used by the R script).
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version

Method Detail

buildScript

List<List<String>> buildScript(List<File> files)
                        throws Exception

Method returns a nested list of bash script lines to classify samples containing forward reads only. The inner list contains the bash script lines required to classify 1 sample.

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

buildScriptForPairedReads

List<List<String>> buildScriptForPairedReads(List<File> files)
                                      throws Exception

Method returns a nested list of bash script lines to classify samples containing paired reads.
The inner list contains the bash script lines required to classify 1 sample.

Parameters:

files - Files in the input directory that contain only paired reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate the script lines

getJobParams

String[] getJobParams()
               throws Exception

Many ScriptModules generate bash or R scripts for the Operating System to run as a Processor.
The Processor creates a Process using the parameters supplied by this method and executed in the Runtime environment.
Parameters typically contain the full script path and script parameters, if needed.

Returns:

Runtime.exec(String) parameters

Throws:

Exception

getMainScript

File getMainScript()
            throws Exception

Method returns MAIN module script that calls each of the worker scripts.

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getScriptDir

File getScriptDir()

ScriptModules that generate scripts to complete their task, create script files in this directory.
The main script must begin with prefix and there must only be one main script.
The main script executes, or submits to the job queue, each of the other scripts in this directory.
The # subscripts generated by the ScriptModule depends upon .

Returns:

File directory containing all ScriptModule scripts

getScriptErrors

List<String> getScriptErrors()
                      throws Exception

Return a list of the error messages saved the failure scripts in the module script directory.

Returns:

List of error messages or empty list

Throws:

Exception - if runtime errors occur

getTimeout

Integer getTimeout()
            throws ConfigFormatException

ScriptModule that run scripts can opt to set a timeout (such as used by the R script).

Returns:

Number of minutes before script is cancelled due to timeout

Throws:

ConfigFormatException - if the value is invalid

getWorkerScriptFunctions

List<String> getWorkerScriptFunctions()
                               throws Exception

Method returns bash script lines used to build the functions called by the worker scripts.

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur