public class DESeq2 extends ScriptModuleImpl implements ApiModule
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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DESeq2() |
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.
|
void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
String |
copyDEseqScript() |
void |
executeTask()
Build the nested list of bash script lines that will be used by
BashScriptBuilder to build
the worker scripts. |
protected List<File> |
findModuleInputFiles()
Called upon first access of input files to return sorted list of files from all
Config ."input.dirPaths"Hidden files (starting with ".") are ignored Call BioModuleImpl.isValidInputModule(BioModule) on each previous module until acceptable input files are found |
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 |
getDetails()
A extension of
getDescription . |
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()
Returns summary message to be displayed by Email module so must not contain confidential info.
|
boolean |
isValidInputModule(BioModule module)
DESeq should only take raw values.
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Boolean |
isValidProp(String property)
Tests to see if the value val is valid for property prop; primarily tests format.
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buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions, hasScripts
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, getAlias, getDescription, getFileCache, getID, getInputFiles, 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, getMenuPlacement, getPropType, getTitle, listProps
cleanUp, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version
protected List<File> findModuleInputFiles()
BioModuleImpl
Config
."input.dirPaths"BioModuleImpl.isValidInputModule(BioModule)
on each previous module until acceptable input files are foundfindModuleInputFiles
in class BioModuleImpl
public void executeTask() throws Exception
ScriptModuleImpl
BashScriptBuilder
to build
the worker scripts. PassBioModuleImpl.getInputFiles()
to either ScriptModuleImpl.buildScript(List)
or
ScriptModuleImpl.buildScriptForPairedReads(List)
based on
Config
."internal.pairedReads".executeTask
in interface BioModule
executeTask
in class ScriptModuleImpl
Exception
- thrown if the module is unable to complete is taskpublic 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 boolean isValidInputModule(BioModule module)
isValidInputModule
in interface BioModule
isValidInputModule
in class BioModuleImpl
module
- BioModule that ran before the current BioModulepublic void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class ScriptModuleImpl
Exception
- thrown if missing or invalid dependencies are foundpublic String getSummary() throws Exception
ScriptModuleImpl
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic Boolean isValidProp(String property) throws Exception
ApiModule
BioModule.checkDependencies()
. Using switch/case or a stack of if/else is recommended.
Within each case, call any/all method that is used by this module to access the value from the config file,
leveraging the checks in the Config.get* methods.
This method should never actually return false. If the value is not valid, it should throw an exception that
includes a helpful message about whats not valid. As part of a throwable, that message is passed along to
wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in
a try/catch.isValidProp
in interface ApiModule
isValidProp
in class ScriptModuleImpl
Exception
public 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 copyDEseqScript() throws IOException, ConfigPathException, DockerVolCreationException
public String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getDetails()
ApiModule
getDescription
. Beyond the brief description, give details such as
the interaction between properties.getDetails
in interface ApiModule
getDetails
in class BioModuleImpl
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule