public class PearMergeReads extends SeqModuleImpl implements ApiModule, ReadCounter
Modifier and Type | Field and Description |
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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"
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static String |
NUM_MERGED_READS
Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"
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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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PearMergeReads() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Build the script lines for each sample as a nested list.
|
void |
checkDependencies()
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void |
cleanUp()
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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.
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String |
getDockerImageTag()
Get the version / tag to use for the docker image.
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String |
getSummary()
Produce summary message with min, max, mean, and median number of reads.
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List<String> |
getWorkerScriptFunctions()
This method generates the required bash functions used by the worker scripts: "mergeReads"
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getInputFiles, getSeqFiles, isValidInputModule
buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
public static final String NUM_MERGED_READS
protected static final String EXE_PEAR
Config
property "exe.pear" defines the command line PEAR executableprotected static final String EXE_PEAR_PARAMS
Config
property "pearMergeReads.pearParams" is used to set the PEAR executable runtime parametersprotected static final String FUNCTION_PEAR_MERGE
public List<List<String>> buildScript(List<File> files) throws Exception
buildScript
in interface ScriptModule
buildScript
in class ScriptModuleImpl
files
- List of module input filesException
- if error occurs generating bash script linespublic void checkDependencies() throws Exception
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic void cleanUp() throws Exception
cleanUp
in interface BioModule
cleanUp
in class BioModuleImpl
Exception
- thrown if any runtime error occurspublic String getSummary() throws Exception
getSummary
in interface BioModule
getSummary
in class SeqModuleImpl
Exception
- if any error occurspublic 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