public abstract class Humann2CountModule extends JavaModuleImpl
BLJ_OPTIONS
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 |
---|
Humann2CountModule() |
Modifier and Type | Method and Description |
---|---|
void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
List<File> |
getInputFiles()
BioModule
BioModuleImpl.getInputFiles() is called to initialize upon first call and cached. |
List<String> |
getPreRequisiteModules()
Module prerequisite:
Humann2Parser |
protected boolean |
isHumann2CountModule(BioModule module)
Check the module to determine if it generated OTU count files.
|
boolean |
isValidInputModule(BioModule module)
If module is a
SeqModule input must contain sequence data. |
buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD, runModule
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
cleanUp, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version
public void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic List<File> getInputFiles()
BioModuleImpl
BioModuleImpl.getInputFiles()
is called to initialize upon first call and cached.getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
public List<String> getPreRequisiteModules() throws Exception
Humann2Parser
getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic boolean isValidInputModule(BioModule module)
JavaModuleImpl
SeqModule
input must contain sequence data.isValidInputModule
in interface BioModule
isValidInputModule
in class JavaModuleImpl
module
- BioModule that ran before the current BioModuleprotected boolean isHumann2CountModule(BioModule module)
module
- BioModule