public class GenomeAssembly extends SeqModuleImpl implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
EXE_CHECKM
Config exe property for checkm executable: "exe.checkm" |
protected static String |
EXE_CHECKM_PARAMS
Config List property used to obtain the checkm runtime parameters: "exe.checkmParams" |
protected static String |
EXE_METABAT2
Config exe property for metabat2 executable: "exe.metabat2" |
protected static String |
EXE_METABAT2_PARAMS
Config List property used to obtain the metabat runtime parameters:
"exe.metabat2Params" |
protected static String |
EXE_METASPADES_PARAMS
Config List property used to obtain the metaspade runtime parameters:
"exe.metaspade2Params" |
protected static String |
EXE_METASPADES2
Config exe property for metaspades executable: "exe.metaspades2" |
protected static String |
FUNCTION_ASSEMBLY
Name of the metaspades function used to assemble reads: "runAssembly"
|
protected static String |
METABAT_MEMORY
Config Positive integer property defines total metabat memory per sample. |
protected static String |
METASPADES_MEMORY
Config Positive integer property defines total metaspades memory per sample. |
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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GenomeAssembly() |
Modifier and Type | Method and Description |
---|---|
List<List<String>> |
buildScript(List<File> files)
Return an inner list of lines to execute for each sample.
|
List<List<String>> |
buildScriptForPairedReads(List<File> files)
MetaSPAdes doesn't require parameters besides input files and output directory.
|
void |
checkDependencies()
Samples must be paired reads since metaspades currently doesn't support single reads.
|
protected String |
getCheckmParams()
Get standard Checkm runtime parameters.
|
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.
|
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.
|
protected String |
getMetabatParams()
Get Metabat runtime parameters.
|
protected String |
getMetaspadeParams()
Get Metaspade runtime parameters.
|
List<String> |
getWorkerScriptFunctions()
Build function to call metaspades, metabat, and Checkm
$1 - forward read $2 - reverse
|
getInputFiles, getSeqFiles, getSummary, 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, getPostRequisiteModules, 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
getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected static final String EXE_CHECKM
Config
exe property for checkm executable: "exe.checkm"protected static final String EXE_CHECKM_PARAMS
Config
List property used to obtain the checkm runtime parameters: "exe.checkmParams"protected static final String EXE_METABAT2
Config
exe property for metabat2 executable: "exe.metabat2"protected static final String EXE_METABAT2_PARAMS
Config
List property used to obtain the metabat runtime parameters:
"exe.metabat2Params"protected static final String EXE_METASPADES_PARAMS
Config
List property used to obtain the metaspade runtime parameters:
"exe.metaspade2Params"protected static final String EXE_METASPADES2
Config
exe property for metaspades executable: "exe.metaspades2"protected static final String FUNCTION_ASSEMBLY
protected static final String METABAT_MEMORY
Config
Positive integer property defines total metabat memory per sample.protected static final String METASPADES_MEMORY
Config
Positive integer property defines total metaspades memory per sample.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<List<String>> buildScriptForPairedReads(List<File> files) throws Exception
buildScriptForPairedReads
in interface ScriptModule
buildScriptForPairedReads
in class ScriptModuleImpl
files
- Files in the input directory that contain only paired readsException
- if errors occurpublic void checkDependencies() throws Exception
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic List<String> getWorkerScriptFunctions() throws Exception
getWorkerScriptFunctions
in interface ScriptModule
getWorkerScriptFunctions
in class ScriptModuleImpl
Exception
- if errors occurprotected String getCheckmParams() throws ConfigException
ConfigException
- if properties are missing or invalidprotected String getMetabatParams() throws ConfigException
ConfigException
- if properties are missing or invalidprotected String getMetaspadeParams() throws ConfigException
ConfigException
- if properties are missing or invalidpublic 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