public interface SeqModule extends ScriptModule
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Modifier and Type | Method and Description |
---|---|
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. |
buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
List<File> getSeqFiles(Collection<File> files) throws SequnceFormatException
Config
."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row.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.