public class Step5 extends Step4
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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Step5() |
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.
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void |
checkDependencies()
Test anything that might cause your module to fail; especially user input.
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String |
getDockerImageName()
Get the docker image to use for this module.
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protected String |
howExciting()
Accesses the "hello.excitmentLevel" and creates a string with that many !s.
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protected String |
makeMessage()
Create a message based on the modules properties.
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getPostRequisiteModules, getPreRequisiteModules, isValidInputModule
isValidProp
getCitationString, getDescription, getDetails
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, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version
public void checkDependencies() throws Exception
Step3.checkDependencies()
Many modules just check properties for unacceptable values.
Some modules may also check than an environment variable is set, or that an executable is reachable, or that some file exists...
This check must be reliable and speedy; otherwise it is very open-ended.checkDependencies
in interface BioModule
checkDependencies
in class Step3
Exception
- thrown if missing or invalid dependencies are foundpublic 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 linesprotected String makeMessage() throws ConfigFormatException
ConfigFormatException
protected String howExciting() throws ConfigFormatException
BioModuleImpl.isValidProp(String)
ConfigFormatException
public String getDockerImageName()
BioModule