Package | Description |
---|---|
biolockj |
The root biolockj package contains core classes used by all BioLockJ pipelines.
|
biolockj.module | |
biolockj.module.classifier |
This package contains Classifier specific
BioModule s that build bash scripts to generate
taxonomy reports from the sequences files. |
biolockj.module.classifier.r16s |
This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences.
Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule . |
biolockj.module.classifier.wgs |
This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data.
As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data. Include the corresponding ParserModule in the Config file to
generate standardized OTU abundance tables. |
biolockj.module.diy | |
biolockj.module.implicit.qiime |
This package contains
BioModule s that are implicitly added to QIIME pipeline as needed. |
biolockj.module.seq |
BioModule s used to prepare sequence files or update the metadata prior to classification. |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
Modifier and Type | Method and Description |
---|---|
static void |
Config.checkDependencies(BioModule module) |
static Map<String,String> |
Config.getEnvVarMap()
Return the String, String map of environment variables and their values.
|
static boolean |
Config.requireBoolean(BioModule module,
String property)
Required to return a valid boolean or
|
static Double |
Config.requireDoubleVal(BioModule module,
String property)
Requires valid double value
|
static File |
Config.requireExistingDir(BioModule module,
String property)
Requires valid existing directory.
|
static List<File> |
Config.requireExistingDirs(BioModule module,
String property)
Requires valid list of file directories
|
static File |
Config.requireExistingFile(BioModule module,
String property)
Require valid existing file
|
static Integer |
Config.requireInteger(BioModule module,
String property)
Requires valid integer value
|
static List<String> |
Config.requireList(BioModule module,
String property)
Require valid list property
|
static Double |
Config.requirePositiveDouble(BioModule module,
String property)
Require valid positive double value
|
static Integer |
Config.requirePositiveInteger(BioModule module,
String property)
Require valid positive integer value
|
static Set<String> |
Config.requireSet(BioModule module,
String property)
Require valid Set value
|
static String |
Config.requireString(BioModule module,
String property)
Require valid String value
|
protected String |
Processor.runJob(String[] args,
String label) |
protected String |
Processor.runJob(String[] args,
String label,
File workDir) |
static void |
Processor.submitJob(String[] args,
String label)
Instantiates a new
Processor .String[] array used to control spacing between command/params. As if executing on terminal args[0] args[1]... |
static String |
Processor.submitQuery(String cmd,
String label)
Run script that expects a single result
|
Modifier and Type | Method and Description |
---|---|
File |
DatabaseModule.getDB()
Return database directory, if multiple databases are configured, they must share a common parent directory and
the common parent directory is returned by this method.
|
Modifier and Type | Method and Description |
---|---|
abstract File |
ClassifierModuleImpl.getDB() |
Modifier and Type | Method and Description |
---|---|
(package private) String |
RdpClassifier.getConfThreshold() |
File |
RdpClassifier.getDB() |
Modifier and Type | Method and Description |
---|---|
File |
Metaphlan2Classifier.getDB() |
File |
Humann2Classifier.getDB() |
File |
KrakenClassifier.getDB() |
File |
Kraken2Classifier.getDB() |
Modifier and Type | Method and Description |
---|---|
protected List<String> |
ForEachLoop.getLoopElements() |
Modifier and Type | Method and Description |
---|---|
File |
QiimeClassifier.getDB()
Check DB parameters for the comment parent directory path, there are 3 parameters:
"qiime.pynastAlignDB"
"qiime.refSeqDB"
"qiime.taxaDB"
|
Modifier and Type | Method and Description |
---|---|
File |
KneadData.getDB() |
Modifier and Type | Method and Description |
---|---|
static boolean |
DemuxUtil.barcodeInHeader()
Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence headers.
|
static boolean |
DemuxUtil.barcodeInMapping()
Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
|
static boolean |
DemuxUtil.barcodeInSeq()
Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.
|
static void |
BashScriptBuilder.checkDependencies(BioModule module) |
static boolean |
BioLockJUtil.copyInputFiles()
Copy input files into an internal folder within the pipeline root direction named "input"
|
static Boolean |
DemuxUtil.doDemux()
Return TRUE if Config is setup to demultiplex the sequence data.
|
static String |
DockerUtil.getDockerImage(BioModule module)
Return the name of the Docker image needed for the given module.
|
static Integer |
ModuleUtil.getMinSamplesPerWorker(BioModule module)
Return the min number of samples that can be processed per worker script.
|
static Integer |
ModuleUtil.getNumWorkers(BioModule module)
Get the actual number of worker scripts generated for a given module, minimum value = 1.
|
static String |
SeqUtil.getSeqType()
Get sequence type
|
protected static String |
BashScriptBuilder.getWorkerScriptPath(ScriptModule module)
Build the file path for the numbered worker script.
|
static List<String> |
TaxaUtil.initTaxaLevels()
Set taxonomy levels ordered by level, from highest to lowest.
|
protected static List<String> |
BashScriptBuilder.passEnvironmentVarVals(ScriptModule module) |
static boolean |
BioLockJUtil.pipelineInputType(String type)
Convenience method to check pipeline input file type.
|
static boolean |
SeqUtil.piplineHasSeqInput()
Return TRUE if pipeline input files are sequence files.
|