public abstract class Step4 extends Step3
EXCITE_PROP, EXCITE_PROP_DESC, NAME_PROP, NAME_PROP_DEFAULT, NAME_PROP_DESC
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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Step4() |
Modifier and Type | Method and Description |
---|---|
List<String> |
getPostRequisiteModules()
By default, no post-requisites are required.
|
List<String> |
getPreRequisiteModules()
By default, no prerequisites are required.
|
boolean |
isValidInputModule(BioModule module)
In the early stages of the pipeline, starting with the very 1st module
ImportMetadata , most modules expect sequence files as input. |
checkDependencies, isValidProp
getCitationString, getDescription, getDetails
buildScript, buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, listProps
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version
public List<String> getPostRequisiteModules() throws Exception
BioModuleImpl
getPostRequisiteModules
in interface BioModule
getPostRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as post-requisitespublic List<String> getPreRequisiteModules() throws Exception
BioModuleImpl
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic boolean isValidInputModule(BioModule module)
BioModuleImpl
ImportMetadata
, most modules expect sequence files as input. This method returns
false if the previousModule only produced a new metadata file, such as
ImportMetadata
or RegisterNumReads
.
When BioModuleImpl.getInputFiles()
is called, this method determines if the previousModule output is valid input for
the current BioModule. The default implementation of this method returns FALSE if the previousModule only
generates a new metadata file.isValidInputModule
in interface BioModule
isValidInputModule
in class BioModuleImpl
module
- BioModule that ran before the current BioModule