biolockj.module.assembly

Class GenomeAssembly

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.assembly.GenomeAssembly

All Implemented Interfaces:

ApiModule, BioModule, ScriptModule, SeqModule, Comparable<BioModule>

public class GenomeAssembly
extends SeqModuleImpl
implements ApiModule

This BioModule builds the bash scripts used to assemble WGS sequences with MetaSPAdes, bin contigs with Metabat2 and check quality with checkM.

GUI Module Name

Genome Assembly

Field Summary

Fields

Modifier and Type	Field and Description
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.

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
GenomeAssembly()

Method Summary

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

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, getSummary, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

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

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version

Methods inherited from interface biolockj.module.ScriptModule

getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

EXE_CHECKM

protected static final String EXE_CHECKM

Config exe property for checkm executable: "exe.checkm"

See Also:

Constant Field Values

EXE_CHECKM_PARAMS

protected static final String EXE_CHECKM_PARAMS

Config List property used to obtain the checkm runtime parameters: "exe.checkmParams"

See Also:

Constant Field Values

EXE_METABAT2

protected static final String EXE_METABAT2

Config exe property for metabat2 executable: "exe.metabat2"

See Also:

Constant Field Values

EXE_METABAT2_PARAMS

protected static final String EXE_METABAT2_PARAMS

Config List property used to obtain the metabat runtime parameters: "exe.metabat2Params"

See Also:

Constant Field Values

EXE_METASPADES_PARAMS

protected static final String EXE_METASPADES_PARAMS

Config List property used to obtain the metaspade runtime parameters: "exe.metaspade2Params"

See Also:

Constant Field Values

EXE_METASPADES2

protected static final String EXE_METASPADES2

Config exe property for metaspades executable: "exe.metaspades2"

See Also:

Constant Field Values

FUNCTION_ASSEMBLY

protected static final String FUNCTION_ASSEMBLY

Name of the metaspades function used to assemble reads: "runAssembly"

See Also:

Constant Field Values

METABAT_MEMORY

protected static final String METABAT_MEMORY

Config Positive integer property defines total metabat memory per sample.

See Also:

Constant Field Values

METASPADES_MEMORY

protected static final String METASPADES_MEMORY

Config Positive integer property defines total metaspades memory per sample.

See Also:

Constant Field Values

Constructor Detail

GenomeAssembly

public GenomeAssembly()

Method Detail

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Description copied from class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

buildScriptForPairedReads

public List<List<String>> buildScriptForPairedReads(List<File> files)
                                             throws Exception

MetaSPAdes doesn't require parameters besides input files and output directory. Default threads is 16 and memory is 250G
Verify no invalid runtime params are passed and add rankSwitch if needed.

Specified by:

buildScriptForPairedReads in interface ScriptModule

Overrides:

buildScriptForPairedReads in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only paired reads

Returns:

runtime parameters

Throws:

Exception - if errors occur

checkDependencies

public void checkDependencies()
                       throws Exception

Samples must be paired reads since metaspades currently doesn't support single reads.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

Build function to call metaspades, metabat, and Checkm $1 - forward read $2 - reverse

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getCheckmParams

protected String getCheckmParams()
                          throws ConfigException

Get standard Checkm runtime parameters.

Returns:

checkm runtime params

Throws:

ConfigException - if properties are missing or invalid

getMetabatParams

protected String getMetabatParams()
                           throws ConfigException

Get Metabat runtime parameters.

Returns:

metabat runtime params

Throws:

ConfigException - if properties are missing or invalid

getMetaspadeParams

protected String getMetaspadeParams()
                             throws ConfigException

Get Metaspade runtime parameters.

Returns:

metaspade runtime parameters

Throws:

ConfigException - if properties are missing or invalid

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns:

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns: