public abstract class OtuCountModule extends JavaModuleImpl
BLJ_OPTIONS
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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OtuCountModule() |
Modifier and Type | Method and Description |
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List<File> |
getInputFiles()
BioModule
BioModuleImpl.getInputFiles() is called to initialize upon first call and cached. |
protected boolean |
isOtuModule(BioModule module)
Check the module to determine if it generated OTU count files.
|
boolean |
isValidInputModule(BioModule module)
If module is a
SeqModule input must contain sequence data. |
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD, runModule
buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
checkDependencies, cleanUp, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version
public List<File> getInputFiles()
BioModuleImpl
BioModuleImpl.getInputFiles()
is called to initialize upon first call and cached.getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
public boolean isValidInputModule(BioModule module)
JavaModuleImpl
SeqModule
input must contain sequence data.isValidInputModule
in interface BioModule
isValidInputModule
in class JavaModuleImpl
module
- BioModule that ran before the current BioModuleprotected boolean isOtuModule(BioModule module)
module
- BioModule