public abstract class SeqModuleImpl extends ScriptModuleImpl implements SeqModule
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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SeqModuleImpl() |
Modifier and Type | Method and Description |
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List<File> |
getInputFiles()
Return
getSeqFiles(Collection) to filter standard module input files. |
List<File> |
getSeqFiles(Collection<File> files)
Return only sequence files for sample IDs found in the metadata file.
If Config ."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row. |
String |
getSummary()
Add database info if module is a DatabaseModule
|
boolean |
isValidInputModule(BioModule module)
In the early stages of the pipeline, starting with the very 1st module
ImportMetadata , most modules expect sequence files as input. |
buildScript, buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageOwner, getDockerImageTag, 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
buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version
public List<File> getInputFiles()
getSeqFiles(Collection)
to filter standard module input files.getInputFiles
in interface BioModule
getInputFiles
in class BioModuleImpl
SequnceFormatException
public List<File> getSeqFiles(Collection<File> files) throws SequnceFormatException
SeqModule
Config
."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row.getSeqFiles
in interface SeqModule
files
- Module input filesSequnceFormatException
- If Config
."metadata.required" =
"Y" but sequence files found that do not have a corresponding record in the metadata
file or if invalid metadata prevents parsing SEQ files.public String getSummary() throws Exception
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic boolean isValidInputModule(BioModule module)
BioModuleImpl
ImportMetadata
, most modules expect sequence files as input. This method returns
false if the previousModule only produced a new metadata file, such as
ImportMetadata
or RegisterNumReads
.
When BioModuleImpl.getInputFiles()
is called, this method determines if the previousModule output is valid input for
the current BioModule. The default implementation of this method returns FALSE if the previousModule only
generates a new metadata file.isValidInputModule
in interface BioModule
isValidInputModule
in class BioModuleImpl
module
- BioModule that ran before the current BioModule