- SAMPLE_ID_SUFFIX_TRIM_DEFAULT - Static variable in class biolockj.module.implicit.Demultiplexer
-
Multiplexed files created by BioLockJ may add sample ID to the sequence header if no barcode is provided.
If sample ID is added, it is immediately followed by the character: "_"
This value can be used then to set
Config.
"input.trimSuffix"
- sampleIdInHeader() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if Config is setup to demultiplex the sequence data based on Sample IDs in the sequence headers.
- sampleIdToQiimeIdMap - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser
-
Convenience map, to convert Sample ID to Qiime ID
- sanitizeMasterConfig() - Static method in class biolockj.util.PropUtil
-
Remove unused properties from the MASTER config file.
- SAVE_CONTAINER_ON_EXIT - Static variable in class biolockj.util.DockerUtil
-
Config property removed the default --rm flag on docker run command if set to TRUE:
"docker.saveContainerOnExit"
- saveEfsDataToS3() - Static method in class biolockj.util.NextflowUtil
-
Save EFS data to S3 based on pipeline Config.
- saveMasterConfig() - Static method in class biolockj.util.PropUtil
-
Save a single version of the Config file with all inherited properties for the default config (if any exist).
- saveMasterConfig(Map<String, String>) - Static method in class biolockj.util.PropUtil
-
Save a single version of the Config file with all inherited properties for the default config (if any exist).
- saveNextflowLog() - Static method in class biolockj.util.NextflowUtil
-
Save a copy of the Nextflow log file to the Pipeline root directory
- saveSummary(String) - Static method in class biolockj.util.SummaryUtil
-
Save the summary generated to the pipeline root directory.
- scanFirstLine(BufferedReader, File) - Static method in class biolockj.util.SeqUtil
-
This method returns the 1st non-empty line and moves the BufferedReader pointer to this line.
- SCRIPT_ADD_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SCRIPT_ADD_LABELS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script that produces
"combined_seqs.fna", the multiplexed fasta file: "add_qiime_labels.py"
- SCRIPT_BATCH_SIZE - Static variable in interface biolockj.module.ScriptModule
-
Config Integer property: "script.batchSize"
Set number of samples to process per script (if parallel processing)
- SCRIPT_CALC_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script that creates alpha diversity metrics file in output/
"alphaDiversity.txt":
"alpha_diversity.py"
- SCRIPT_DEFAULT_HEADER - Static variable in interface biolockj.module.ScriptModule
-
Config List property: "script.defaultHeader"
Store default script header for MAIN script and locally run WORKER scripts.
- SCRIPT_DIR - Static variable in class biolockj.Constants
-
Name of the script sub-directory: "script"
- SCRIPT_FAILURES - Static variable in class biolockj.Constants
-
File suffix appended to failed scripts: "Failures"
- SCRIPT_FILTER_OTUS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script used to remove chimeras detected by
"exe.vsearch": "filter_otus_from_otu_table.py"
- SCRIPT_JOB_HEADER - Static variable in class biolockj.util.BashScriptBuilder
-
Config String property: "cluster.jobHeader"
Header written at top of worker scripts
- SCRIPT_MERGE_OTU_TABLES - Static variable in class biolockj.module.implicit.qiime.MergeQiimeOtuTables
-
QIIME script to merge multiple OTU tables in biom format.
- SCRIPT_NUM_THREADS - Static variable in interface biolockj.module.ScriptModule
-
Config Integer property: "script.numThreads"
Used to reserve cluster resources and passed to any external application call that accepts a numThreads
parameter.
- SCRIPT_PERMISSIONS - Static variable in interface biolockj.module.ScriptModule
-
Config String property: "script.permissions"
Used as chmod permission parameter (ex: 774)
- SCRIPT_PRINT_CONFIG - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script to print environment configuration to qsub output file: "print_qiime_config.py"
- SCRIPT_STARTED - Static variable in class biolockj.Constants
-
File suffix appended to started script: "Started"
- SCRIPT_SUCCESS - Static variable in class biolockj.Constants
-
File suffix appended to successful scripts: "Success"
- SCRIPT_SUMMARIZE_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SCRIPT_SUMMARIZE_TAXA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script used to produce taxonomy-level reports in the module output directory:
"summarize_taxa.py"
- SCRIPT_TIMEOUT - Static variable in interface biolockj.module.ScriptModule
-
Config Integer property: "script.timeout"
Sets # of minutes before worker scripts times out.
- SCRIPT_VALIDATE_MAPPING - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping
-
QIIME script used to validate the QIIME mapping file format
- ScriptModule - Interface in biolockj.module
-
Classes that implement this interface are
- ScriptModuleImpl - Class in biolockj.module
-
Superclass for Java BioModules that will be called in separate instances of the application.
- ScriptModuleImpl() - Constructor for class biolockj.module.ScriptModuleImpl
-
- SEPARATOR - Static variable in class biolockj.Constants
-
Semi-colon is used to separate each taxa "|"
- SeqFileValidator - Class in biolockj.module.seq
-
This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
- SeqFileValidator() - Constructor for class biolockj.module.seq.SeqFileValidator
-
- SeqModule - Interface in biolockj.module
-
Classes that implement this interface requires sequence files for input.
- SeqModuleImpl - Class in biolockj.module
-
Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.
- SeqModuleImpl() - Constructor for class biolockj.module.SeqModuleImpl
-
- SeqUtil - Class in biolockj.util
-
This utility helps interact with FastA and FastQ sequence files.
- setConfigProperty(String, Collection<?>) - Static method in class biolockj.Config
-
Sets a property value in the props cache as a list
- setConfigProperty(String, String) - Static method in class biolockj.Config
-
Sets a property value in the props cache
- setCount(int) - Method in interface biolockj.node.OtuNode
-
Set the number of reads for a sample ID that have this OTU assignment.
- setCount(int) - Method in class biolockj.node.OtuNodeImpl
-
- setFile(File) - Static method in class biolockj.util.MetaUtil
-
Set a new metadata file.
- setFilePermissions(String, String) - Static method in class biolockj.Processor
-
- setLevel(String) - Method in class biolockj.node.JsonNode
-
Setter method for level
- setLine(String) - Method in interface biolockj.node.OtuNode
-
Set the classifier report line parsed to build this OTU node.
- setLine(String) - Method in class biolockj.node.OtuNodeImpl
-
Set line only if in DEBUG mode, so we can print OtuNode constructor inputs.
- setMultiplexedConfig() - Method in class biolockj.module.implicit.Demultiplexer
-
- setNumHitsFieldName(String) - Static method in class biolockj.module.implicit.parser.ParserModuleImpl
-
When a module modifies the number of hits, the new counts must replace the old count fields.
- setNumReadFieldName(String) - Static method in class biolockj.module.implicit.RegisterNumReads
-
When a module modifies the number of reads, the new counts must replace the old count fields.
- setOrderedQiimeIDs(File) - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
-
- setParent(JsonNode) - Method in class biolockj.node.JsonNode
-
Setter method for parent
- setPipelineDir(File) - Static method in class biolockj.Config
-
Set the root pipeline directory path
- setPipelineInputFiles(List<File>) - Static method in class biolockj.util.BioLockJUtil
-
Setter for pipeline input files.
- setPipelineRootDir() - Static method in class biolockj.Config
-
Set Create a pipeline root directory if the pipeline is new.
- setSampleId(String) - Method in interface biolockj.node.OtuNode
-
Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.
- setSampleId(String) - Method in class biolockj.node.OtuNodeImpl
-
- setTaxa(String) - Method in class biolockj.node.JsonNode
-
Setter method for taxa
- SH_EXT - Static variable in class biolockj.Constants
-
BioLockJ shell script file extension constant: ".sh"
- SH_EXT - Static variable in class biolockj.module.BioModuleImpl
-
BioLockJ shell script file extension constant: ".sh"
- SILVA_CLASS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva class taxonomy level delimiter: "D_2__"
- SILVA_DOMAIN_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva domain taxonomy level delimiter: "D_0__"
- SILVA_FAMILY_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva family taxonomy level delimiter: "D_4__"
- SILVA_GENUS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva genus taxonomy level delimiter: "D_5__"
- SILVA_ORDER_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva order taxonomy level delimiter: "D_3__"
- SILVA_PHYLUM_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva phylum taxonomy level delimiter: "D_1__"
- SILVA_SPECIES_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva species taxonomy level delimiter: "D_6__"
- SPAWN_DOCKER_CONTAINER - Static variable in class biolockj.util.DockerUtil
-
Name of the bash script function used to generate a new Docker container: "spawnDockerContainer"
- SPECIES - Static variable in class biolockj.Constants
-
- SPECIES_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for SPECIES
- STANDARD_CONFIG_PATH - Static variable in class biolockj.Constants
-
Default
Config imported for all pipelines (if file exists)
- startNextflow(List<BioModule>) - Static method in class biolockj.util.NextflowUtil
-
Call this method to build the Nextflow main.nf for the current pipeline.
- startPipeline() - Static method in class biolockj.Pipeline
-
This method initializes and executes the BioModules set in the BioLockJ configuration file.
- subDirExists(BioModule, String) - Static method in class biolockj.util.ModuleUtil
-
Return TRUE if BioModule sub-directory exists
- submit(ScriptModule) - Static method in class biolockj.Processor
-
This method is called by script generating
ScriptModules to update the script
file-permissions to ensure they are executable by the program.
- submit(String[], String) - Static method in class biolockj.Processor
-
Instantiates a new
Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]...
- SubProcess(String[], String) - Constructor for class biolockj.Processor.SubProcess
-
Execute the command args in a separate thread and log output with label.
- SUMMARIZE_TAXA_SUPPRESS_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SUMMARY - Static variable in class biolockj.module.report.otu.CompileOtuCounts
-
Output file prefix: "summary"
- SummaryUtil - Class in biolockj.util
-
This module builds an execution summary for the pipeline which is printed to the log file and is be sent to the user
if the Email module is configured.
- SummaryUtil() - Constructor for class biolockj.util.SummaryUtil
-
- syncModuleLogs(ScriptModule) - Static method in class biolockj.util.LogUtil
-
Not used currently.