biolockj.module

Interface JavaModule

All Superinterfaces:

BioModule, ScriptModule

All Known Subinterfaces:

ParserModule

All Known Implementing Classes:

AddMetadataToPathwayTables, AddMetadataToTaxaTables, BuildTaxaTables, CompileOtuCounts, Demultiplexer, Humann2CountModule, Humann2Parser, JavaModuleImpl, JsonReport, Kraken2Parser, KrakenParser, LogTransformTaxaTables, Metaphlan2Parser, Multiplexer, NormalizeTaxaTables, OtuCountModule, ParserModuleImpl, QiimeParser, RarefyOtuCounts, RarefySeqs, RdpParser, RegisterNumReads, RemoveLowOtuCounts, RemoveLowPathwayCounts, RemoveScarceOtuCounts, RemoveScarcePathwayCounts, SeqFileValidator, TaxaCountModule, TrimPrimers

public interface JavaModule
extends ScriptModule

Classes that implement this interface are pure Java modules.

Field Summary

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
void	moduleComplete() This method will create the success flag file so the next module can run.
void	moduleFailed() This method will create the fail flag file so the pipeline can move on..
void	runModule() This method executes the modules primary Java routine.

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getSummary, getTempDir, init, isValidInputModule

Method Detail

moduleComplete

void moduleComplete()
             throws Exception

This method will create the success flag file so the next module can run.

Throws:

Exception - thrown if any runtime error occurs

moduleFailed

void moduleFailed()
           throws Exception

This method will create the fail flag file so the pipeline can move on..

Throws:

Exception - thrown if any runtime error occurs

runModule

void runModule()
        throws Exception

This method executes the modules primary Java routine.

Throws:

Exception - thrown if any runtime error occurs