public class ForEachSample extends GenMod
CODE_LINE, LAUNCHER, PARAM, RESOURCES, SCRIPT
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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ForEachSample() |
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 |
getDetails()
A extension of
getDescription . |
List<File> |
getInputFiles()
Supply a list with the correct number of files to match the number of inputs.
|
String |
version()
Changes to a module class should be accompanied by a increment in version.
|
checkDependencies, getDockerImageName, getDockerImageOwner, getDockerImageTag, getInputDataTypes, getLauncher, getScriptParams, isValidProp, transferResources, transferScript
buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, 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, getMenuPlacement, getPropType, getTitle, listProps
cleanUp, executeTask, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias
public List<List<String>> buildScript(List<File> files) throws Exception
ScriptModuleImpl
buildScript
in interface ScriptModule
buildScript
in class GenMod
files
- Files in the input directory that contain only forward readsException
- if unable to generate script linespublic List<File> getInputFiles()
getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
getDescription
in class GenMod
public String getDetails() throws API_Exception
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class GenMod
API_Exception
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
getCitationString
in class GenMod