biolockj.module.seq

Class PearMergeReads

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.PearMergeReads

All Implemented Interfaces:

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

public class PearMergeReads
extends SeqModuleImpl
implements ApiModule, ReadCounter

This BioModule will merge forward and reverse fastq files using PEAR.
For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html

GUI Module Name

Merge Reads with PEAR

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_PEAR Config property "exe.pear" defines the command line PEAR executable
protected static String	EXE_PEAR_PARAMS Config property "pearMergeReads.pearParams" is used to set the PEAR executable runtime parameters
protected static String	FUNCTION_PEAR_MERGE Name of the bash function that merges files with PEAR: "mergeReads"
static String	NUM_MERGED_READS Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"

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
PearMergeReads()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build the script lines for each sample as a nested list.
void	checkDependencies() Validate module dependencies Verify input files are in fastq format Verify matching paired reads are found Validate required Config.EXE_PEAR property If running a restarted pipeline that already merged reads, set paired indicator to false
void	cleanUp() Set Config."internal.pairedReads" = "N" and register number of reads.
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.
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
List<String>	getWorkerScriptFunctions() This method generates the required bash functions used by the worker scripts: "mergeReads"

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, 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

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

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

NUM_MERGED_READS

public static final String NUM_MERGED_READS

Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"

See Also:

Constant Field Values

EXE_PEAR

protected static final String EXE_PEAR

Config property "exe.pear" defines the command line PEAR executable

See Also:

Constant Field Values

EXE_PEAR_PARAMS

protected static final String EXE_PEAR_PARAMS

Config property "pearMergeReads.pearParams" is used to set the PEAR executable runtime parameters

See Also:

Constant Field Values

FUNCTION_PEAR_MERGE

protected static final String FUNCTION_PEAR_MERGE

Name of the bash function that merges files with PEAR: "mergeReads"

See Also:

Constant Field Values

Constructor Detail

PearMergeReads

public PearMergeReads()

Method Detail

buildScript

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

Build the script lines for each sample as a nested list. PAIR program will be called once for each pair of files to output a single merged read.

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - List of module input files

Returns:

List of nested bash script lines.

Throws:

Exception - if error occurs generating bash script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies

1. Verify input files are in fastq format
2. Verify matching paired reads are found
3. Validate required Config.EXE_PEAR property
4. If running a restarted pipeline that already merged reads, set paired indicator to false

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

Set Config."internal.pairedReads" = "N" and register number of reads.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getSummary

public String getSummary()
                  throws Exception

Produce summary message with min, max, mean, and median number of reads.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the required bash functions used by the worker scripts: "mergeReads"

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

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: