public class Hello_World extends ScriptModuleImpl 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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Hello_World() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Return an inner list of lines to execute for each sample.
|
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 |
getDockerImageName()
Get the docker image to use for this module.
|
List<String> |
getWorkerScriptFunctions()
Method returns bash script lines used to build the functions called by the worker scripts.
|
buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageOwner, getDockerImageTag, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
public List<List<String>> buildScript(List<File> files) throws Exception
ScriptModuleImpl
buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic List<String> getWorkerScriptFunctions() throws Exception
ScriptModule
getWorkerScriptFunctions
in interface ScriptModule
getWorkerScriptFunctions
in class ScriptModuleImpl
Exception
- if errors occurpublic String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule