public class Stop extends BioModuleImpl implements ApiModule
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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Stop() |
Modifier and Type | Method and Description |
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void |
checkDependencies()
If restarting or running a direct pipeline execute the cleanup for completed modules.
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void |
executeTask()
This is the main method called when it is time for the BioModule to complete its task.
|
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDescription()
Briefly describe what this module does.
|
String |
getDetails()
A extension of
getDescription . |
String |
getDockerImageName()
Get the docker image to use for this module.
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String |
getDockerImageOwner()
Get the name of the docker hub user that owns the image to use for this module.
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String |
version()
Changes to a module class should be accompanied by a increment in version.
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addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getSummary, getTempDir, getTitle, hashCode, init, isValidInputModule, isValidProp, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, getAlias, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias
public Stop() throws PipelineFormationException
PipelineFormationException
public String getDockerImageOwner()
BioModule
getDockerImageOwner
in interface BioModule
getDockerImageOwner
in class BioModuleImpl
public String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public void checkDependencies() throws Exception
BioModuleImpl
checkDependencies
in interface BioModule
checkDependencies
in class BioModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic void executeTask() throws Exception
BioModule
executeTask
in interface BioModule
executeTask
in class BioModuleImpl
Exception
- thrown if the module is unable to complete is taskpublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule