biolockj.module

Interface SeqModule

All Superinterfaces:

BioModule, ScriptModule

All Known Subinterfaces:

ClassifierModule

All Known Implementing Classes:

AwkFastaConverter, BuildQiimeMapping, ClassifierModuleImpl, Demultiplexer, GenomeAssembly, Gunzipper, Humann2Classifier, KneadData, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, Multiplexer, PearMergeReads, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, RarefySeqs, RdpClassifier, RegisterNumReads, SeqFileValidator, SeqModuleImpl, TrimPrimers

public interface SeqModule
extends ScriptModule

Classes that implement this interface requires sequence files for input.

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<File>	getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

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

Method Detail

getSeqFiles

List<File> getSeqFiles(Collection<File> files)
                throws SequnceFormatException

Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Parameters:

files - Module input files

Returns:

Module sequence files

Throws:

SequnceFormatException - If Config."metadata.required" = "Y" but sequence files found that do not have a corresponding record in the metadata file or if invalid metadata prevents parsing SEQ files.