public class Gunzipper extends SeqModuleImpl implements ApiModule
Modifier and Type | Field and Description |
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protected static String |
FUNCTION_GUNZIP
Name of the bash function used to decompress gzipped files: "openZip"
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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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Gunzipper() |
Modifier and Type | Method and Description |
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List<List<String>> |
buildScript(List<File> files)
Return an inner list of lines to execute for each sample.
|
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.
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List<String> |
getWorkerScriptFunctions()
This method generates the bash function: "openZip".
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getInputFiles, getSeqFiles, getSummary, isValidInputModule
buildScriptForPairedReads, checkDependencies, 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
checkDependencies, cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout
protected static final String FUNCTION_GUNZIP
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<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