public class Kraken2Classifier extends ClassifierModuleImpl implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
EXE_KRAKEN2
Config exe property for kraken2 executable: "exe.kraken2" |
protected static String |
FUNCTION_KRAKEN
Name of the kraken function used to assign taxonomy: "runKraken2"
|
protected static String |
KRAKEN_DATABASE
Config property must contain file path to Kraken kmer database directory:
"kraken2.db" |
protected static String |
KRAKEN_FILE
File suffix added by BioLockJ to kraken output files (before translation): "_kraken2_out.txt"
|
protected static String |
KRAKEN2_PARAMS |
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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Kraken2Classifier() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Build bash script lines to classify unpaired WGS reads with Kraken2.
|
List<List<String>> |
buildScriptForPairedReads(List<File> files)
Build bash script lines to classify paired WGS reads with Kraken.
|
void |
checkDependencies()
Verify that none of the derived command line parameters are included in
Config ."exe.kraken2". |
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getClassifierExe()
Get kraken executable command: "exe.kraken2"
|
List<String> |
getClassifierParams()
Obtain the kraken2 runtime params
|
File |
getDB()
Return database directory, if multiple databases are configured, they must share a common parent directory and
the common parent directory is returned by this method.
|
String |
getDescription()
Briefly describe what this module does.
|
String |
getDockerImageName()
Get the docker image to use for this module.
|
String |
getDockerImageOwner()
Get the name of the docker hub user that owns the image to use for this module.
|
String |
getDockerImageTag()
Get the version / tag to use for the docker image.
|
List<String> |
getWorkerScriptFunctions()
This method generates the required bash function: "runKraken2"
|
getClassifierType, getDbCache, getPostRequisiteModules, getSummary, setDbCache, validateModuleOrder
getInputFiles, getSeqFiles, isValidInputModule
executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
getSeqFiles
getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected static final String EXE_KRAKEN2
Config
exe property for kraken2 executable: "exe.kraken2"protected static final String FUNCTION_KRAKEN
protected static final String KRAKEN_DATABASE
Config
property must contain file path to Kraken kmer database directory:
"kraken2.db"protected static final String KRAKEN2_PARAMS
protected static final String KRAKEN_FILE
public List<List<String>> buildScript(List<File> files) throws Exception
Example lines:
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<List<String>> buildScriptForPairedReads(List<File> files) throws Exception
Example lines:
buildScriptForPairedReads
in interface ScriptModule
buildScriptForPairedReads
in class ScriptModuleImpl
files
- Files in the input directory that contain only paired readsException
- if unable to generate the script linespublic void checkDependencies() throws Exception
Config
."exe.kraken2".checkDependencies
in interface BioModule
checkDependencies
in class ClassifierModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic String getClassifierExe() throws ConfigException
getClassifierExe
in interface ClassifierModule
getClassifierExe
in class ClassifierModuleImpl
ConfigException
- if Configuration errors are thrownpublic List<String> getClassifierParams() throws ConfigException
getClassifierParams
in interface ClassifierModule
getClassifierParams
in class ClassifierModuleImpl
ConfigException
- if Configuration errors are thrownpublic File getDB() throws ConfigNotFoundException, ConfigPathException, DockerVolCreationException
DatabaseModule
getDB
in interface DatabaseModule
getDB
in class ClassifierModuleImpl
ConfigNotFoundException
- if DB property is undefined and the default DB is not included in the module
runtime envConfigPathException
- if path is defined but does not existsDockerVolCreationException
public List<String> getWorkerScriptFunctions() throws Exception
getWorkerScriptFunctions
in interface ScriptModule
getWorkerScriptFunctions
in class ScriptModuleImpl
Exception
- if errors occurpublic String getDockerImageOwner()
BioModule
getDockerImageOwner
in interface BioModule
getDockerImageOwner
in class BioModuleImpl
public String getDockerImageName()
BioModule
getDockerImageName
in interface BioModule
public String getDockerImageTag()
BioModule
getDockerImageTag
in interface BioModule
getDockerImageTag
in class BioModuleImpl
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule