- cacheInputFiles(Collection<File>) - Method in class biolockj.module.BioModuleImpl
-
- calcTimeout(List<File>) - Method in class biolockj.module.report.r.R_Module
-
Use this to estimate the max time needed to process a given list of inputs.
- cancel() - Method in class biolockj.launch.LabeledSpinner
-
- catchFirstResponse(Process) - Method in class biolockj.launch.LaunchProcess
-
- checkBasicArgCompatibility() - Method in class biolockj.launch.LaunchProcess
-
- checkDependencies(BioModule) - Static method in class biolockj.Config
-
- checkDependencies() - Method in class biolockj.module.assembly.GenomeAssembly
-
Samples must be paired reads since metaspades currently doesn't support single reads.
- checkDependencies() - Method in interface biolockj.module.BioModule
-
During pipeline initialization, all configured BioModules will run this method to validate dependencies.
- checkDependencies() - Method in class biolockj.module.BioModuleImpl
-
If restarting or running a direct pipeline execute the cleanup for completed modules.
- checkDependencies() - Method in class biolockj.module.classifier.ClassifierModuleImpl
-
- checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
-
Call
QiimeClassifier
checkOtuPickingDependencies() method to verify OTU
picking script parameters.
- checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier
-
Call
QiimeClassifier
checkOtuPickingDependencies() method to verify OTU
picking script parameters.
- checkDependencies() - Method in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier
-
Call
QiimeClassifier
checkOtuPickingDependencies() method to verify OTU
picking script parameters.
- checkDependencies() - Method in class biolockj.module.classifier.r16s.RdpClassifier
-
- checkDependencies() - Method in class biolockj.module.classifier.wgs.Humann2Classifier
-
- checkDependencies() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier
-
- checkDependencies() - Method in class biolockj.module.classifier.wgs.KrakenClassifier
-
Verify that none of the derived command line parameters are included in
Config
.
"exe.kraken".
- checkDependencies() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier
-
- checkDependencies() - Method in class biolockj.module.diy.ForEachLoop
-
- checkDependencies() - Method in class biolockj.module.diy.GenMod
-
- checkDependencies() - Method in class biolockj.module.diy.Rmarkdown
-
- checkDependencies() - Method in class biolockj.module.getData.sra.SraDownload
-
- checkDependencies() - Method in class biolockj.module.getData.sra.SraMetaData
-
- checkDependencies() - Method in class biolockj.module.getData.sra.SraMetaDB
-
- checkDependencies() - Method in class biolockj.module.hello_world.Hello_Friends
-
Be sure to touch any / all properties your module uses.
- checkDependencies() - Method in class biolockj.module.hello_world.Step3
-
Be sure to touch any / all properties your module uses.
- checkDependencies() - Method in class biolockj.module.hello_world.Step5
-
Test anything that might cause your module to fail; especially user input.
- checkDependencies() - Method in class biolockj.module.implicit.Demultiplexer
-
- checkDependencies() - Method in class biolockj.module.implicit.ImportMetadata
-
- checkDependencies() - Method in class biolockj.module.implicit.parser.ParserModuleImpl
-
- checkDependencies() - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser
-
- checkDependencies() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
- checkDependencies() - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables
-
- checkDependencies() - Method in class biolockj.module.implicit.qiime.QiimeClassifier
-
- checkDependencies() - Method in class biolockj.module.report.Email
-
Verify required email
Config
properties exist and are properly formatted.
- checkDependencies() - Method in class biolockj.module.report.humann2.Humann2CountModule
-
- checkDependencies() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts
-
- checkDependencies() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts
-
- checkDependencies() - Method in class biolockj.module.report.otu.RarefyOtuCounts
-
- checkDependencies() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
-
- checkDependencies() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
- checkDependencies() - Method in class biolockj.module.report.r.R_CalculateStats
-
- checkDependencies() - Method in class biolockj.module.report.r.R_Module
-
- checkDependencies() - Method in class biolockj.module.report.r.R_PlotEffectSize
-
At least one of the available plot types should NOT be disabled.
- checkDependencies() - Method in class biolockj.module.report.r.R_PlotMds
-
- checkDependencies() - Method in class biolockj.module.report.r.R_PlotOtus
-
- checkDependencies() - Method in class biolockj.module.report.r.R_PlotPvalHistograms
-
- checkDependencies() - Method in class biolockj.module.report.taxa.LogTransformTaxaTables
-
- checkDependencies() - Method in class biolockj.module.rnaseq.DESeq2
-
- checkDependencies() - Method in class biolockj.module.rnaseq.EdgeR
-
- checkDependencies() - Method in class biolockj.module.ScriptModuleImpl
-
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
- checkDependencies() - Method in class biolockj.module.seq.KneadData
-
- checkDependencies() - Method in class biolockj.module.seq.Multiplexer
-
Validate module dependencies:
Validate this is the last module to run (excluding
Email
)
If this module was completed on a previous run, update the property:
Config
.
"internal.multiplexed" =
"Y"
- checkDependencies() - Method in class biolockj.module.seq.PearMergeReads
-
Validate module dependencies
Verify input files are in fastq format
Verify matching paired reads are found
Validate required
Config
.
PearMergeReads.EXE_PEAR
property
If running a restarted pipeline that already merged reads, set paired indicator to false
- checkDependencies() - Method in class biolockj.module.seq.RarefySeqs
-
- checkDependencies() - Method in class biolockj.module.seq.SeqFileValidator
-
- checkDependencies() - Method in class biolockj.module.seq.TrimPrimers
-
Validates the file that defines the REGEX primers.
- checkDependencies() - Method in class biolockj.module.Stop
-
- checkDependencies(BioModule) - Static method in class biolockj.util.BashScriptBuilder
-
- checkDependencies(BioModule) - Static method in class biolockj.util.DockerUtil
-
- checkDependencies(BioModule) - Static method in class biolockj.util.ValidationUtil
-
This method calls the methods that are used by executeTask to get the validation input.
- checkModuleDependencies() - Static method in class biolockj.Pipeline
-
- checkOneModulesDependencies(BioModule) - Static method in class biolockj.Pipeline
-
- checkVersion() - Static method in class biolockj.util.BioLockJUtil
-
- CITE_QIIME - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- CLASS - Static variable in class biolockj.Constants
-
- CLASS_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for CLASS
- ClassifierModule - Interface in biolockj.module.classifier
-
Classifier
BioModule
s build one or more bash scripts to call the application on sequence
files.
- ClassifierModuleImpl - Class in biolockj.module.classifier
-
This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.
- ClassifierModuleImpl() - Constructor for class biolockj.module.classifier.ClassifierModuleImpl
-
- classifyReportableMetadata(BioModule) - Static method in class biolockj.util.RMetaUtil
-
Classify and verify the R filter and reportable metadata fields listed in the
Config
file.
All metadata fields are reported unless specific fields are listed in:
Config
.
"r.reportFields".
- cleanUp() - Method in interface biolockj.module.BioModule
-
This method executes after execution to update Config modified by the module or other cleanup operations.
- cleanUp() - Method in class biolockj.module.BioModuleImpl
-
If metadata exists in module output directory, refresh MetaUtil.
- cleanUp() - Method in class biolockj.module.classifier.wgs.Humann2Classifier
-
- cleanUp() - Method in class biolockj.module.getData.sra.SraDownload
-
- cleanUp() - Method in class biolockj.module.getData.sra.SrpSrrConverter
-
- cleanUp() - Method in class biolockj.module.implicit.Demultiplexer
-
Update SeqUtil to indicate data has been demultiplexed.
- cleanUp() - Method in class biolockj.module.implicit.ImportMetadata
-
Verify the metadata fields configured for R reports.
- cleanUp() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
-
- cleanUp() - Method in class biolockj.module.implicit.qiime.QiimeClassifier
-
The cleanUp operation builds a new metadata file if alpha diversity metrics were generated by this module.
- cleanUp() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables
-
For R to report HumanN2 reports instead of taxa levels
- cleanUp() - Method in class biolockj.module.report.otu.RarefyOtuCounts
-
- cleanUp() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
-
- cleanUp() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts
-
Set the number of hits field.
- cleanUp() - Method in class biolockj.module.report.r.R_Module
-
- cleanUp() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables
-
For R to report taxa levels (not HumanN2 reports)
- cleanUp() - Method in class biolockj.module.seq.AwkFastaConverter
-
- cleanUp() - Method in class biolockj.module.seq.PearMergeReads
-
- cleanUp() - Method in class biolockj.module.seq.RarefySeqs
-
- cleanUp() - Method in class biolockj.module.seq.SeqFileValidator
-
- cleanUp() - Method in class biolockj.module.seq.TrimPrimers
-
- clear() - Static method in class biolockj.launch.ProgressUtil
-
Use with caution.
- clearDemuxConfig() - Static method in class biolockj.util.DemuxUtil
-
Clear demultiplexer related fields
- clearStatus(File) - Static method in class biolockj.pipelines.PipelineUtil
-
Remove the current status flag of a given directory
- clearStatus(String) - Static method in class biolockj.pipelines.PipelineUtil
-
Remove the current status flag of a given directory
- CLUSTER_BATCH_COMMAND - Static variable in class biolockj.util.BashScriptBuilder
-
Config
String property: "cluster.batchCommand"
- CLUSTER_HAS_BATCH_IDS - Static variable in class biolockj.util.BashScriptBuilder
-
Config
Boolean property: "cluster.returnsBatchIds"
- CLUSTER_HOST - Static variable in class biolockj.Constants
-
- CLUSTER_MODULES - Static variable in class biolockj.util.BashScriptBuilder
-
Config
List property: "cluster.modules"
- CLUSTER_NUM_PROCESSORS - Static variable in class biolockj.util.BashScriptBuilder
-
- CLUSTER_PROLOGUE - Static variable in class biolockj.util.BashScriptBuilder
-
Config
String property: "cluster.prologue"
- CLUSTER_STATUS_COMMAND - Static variable in class biolockj.util.BashScriptBuilder
-
Config
String property: "cluster.statusCommand"
- CODE_LINE - Static variable in class biolockj.module.diy.GenMod
-
- COMBINED_FNA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- command - Variable in class biolockj.launch.LaunchProcess
-
- COMMON_CAUSES - Static variable in exception biolockj.exception.PipelineScriptException
-
- CommonDockerMapper - Class in biolockj.util.paths
-
Introduced with BioLockJ v1.3.18.
- CommonDockerMapper() - Constructor for class biolockj.util.paths.CommonDockerMapper
-
- COMPARE_ON - Static variable in class biolockj.util.ValidationUtil
-
Config
set property giving the file metrics to use in comparing to the expectation.
- compareTo(BioModule) - Method in class biolockj.module.BioModuleImpl
-
- compareTo(JsonNode) - Method in class biolockj.node.JsonNode
-
- compareTo(OtuNode) - Method in class biolockj.node.OtuNodeImpl
-
- compareTo(ParsedSample) - Method in class biolockj.node.ParsedSample
-
- CompileOtuCounts - Class in biolockj.module.report.otu
-
This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU
counts for the entire dataset.
- CompileOtuCounts() - Constructor for class biolockj.module.report.otu.CompileOtuCounts
-
- compileOtuCounts(Collection<File>) - Method in class biolockj.module.report.otu.CompileOtuCounts
-
Compile OTU counts from the individual sample OTU count files
- compileSampleOtuCounts(File) - Static method in class biolockj.util.OtuUtil
-
Compile OTU counts from an individual sample OTU count file
- Config - Class in biolockj
-
Provides type-safe, validated methods for storing/accessing system properties.
Initially populated by the properties in the Config file, several additional properties are created and stored in the
the Config (to save system determined info such as: pipeline directory and name, has paired reads?, has multiplexed
reads?, etc.).
- Config() - Constructor for class biolockj.Config
-
- CONFIG_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- CONFIG_FILE - Static variable in class biolockj.util.RuntimeParamUtil
-
Config
file path runtime parameter switch: "-config"
- ConfigConflictException - Exception in biolockj.exception
-
- ConfigConflictException(String) - Constructor for exception biolockj.exception.ConfigConflictException
-
- ConfigConflictException(String, String) - Constructor for exception biolockj.exception.ConfigConflictException
-
- ConfigConflictException(String[], String) - Constructor for exception biolockj.exception.ConfigConflictException
-
- ConfigException - Exception in biolockj.exception
-
ConfigException is the superclass for all BioLockJ configuration file Exceptions used to ensure message uniformity.
- ConfigException(String) - Constructor for exception biolockj.exception.ConfigException
-
Abstract
Config
exception calls super to instantiate using the superclass
Exception
implementation
- ConfigException(String, String) - Constructor for exception biolockj.exception.ConfigException
-
- ConfigFormatException - Exception in biolockj.exception
-
ConfigFormatException is thrown if property is defined but the format is invalid.
- ConfigFormatException(String, String) - Constructor for exception biolockj.exception.ConfigFormatException
-
ConfigFormatException is thrown if property is defined but the format is invalid.
- ConfigNotFoundException - Exception in biolockj.exception
-
ConfigNotFoundException is thrown if a required
Config
property is undefined.
- ConfigNotFoundException(String) - Constructor for exception biolockj.exception.ConfigNotFoundException
-
ConfigNotFoundException is thrown if a required
Config
property is undefined.
- ConfigNotFoundException(String, String) - Constructor for exception biolockj.exception.ConfigNotFoundException
-
ConfigNotFoundException is thrown if a required
Config
property is undefined.
- ConfigPathException - Exception in biolockj.exception
-
ConfigPathException is thrown if property is invalid file paths are encountered when processing the BioLockJ
configuration file.
- ConfigPathException(File) - Constructor for exception biolockj.exception.ConfigPathException
-
ConfigPathException is thrown if the filePath parameter does not exist on the file system.
- ConfigPathException(File, String) - Constructor for exception biolockj.exception.ConfigPathException
-
ConfigPathException is thrown if the filePath parameter does not exist on the file system.
- ConfigPathException(String, String) - Constructor for exception biolockj.exception.ConfigPathException
-
ConfigPathException is thrown if the path does not exist or is not the proper file type:
"file" or
"directory".
- ConfigViolationException - Exception in biolockj.exception
-
ConfigViolationException is thrown at runtime due to application state violations caused by invalid module I/O
(sequences or metadata) as defined by
Config
properties.
- ConfigViolationException(String) - Constructor for exception biolockj.exception.ConfigViolationException
-
Generic exception message.
- ConfigViolationException(String, String) - Constructor for exception biolockj.exception.ConfigViolationException
-
ConfigViolationException is thrown application detects a violation due to a
Config
property
setting, such as finding Sample IDs with no corresponding sequence file enforced by
Config
.
"metadata.useEveryRow" =
"Y"
- Constants - Class in biolockj
-
Single Java class to hold shared constant values referenced my multiple classes.
- Constants() - Constructor for class biolockj.Constants
-
- CONTAINER_BLJ_DIR - Static variable in class biolockj.util.DockerUtil
-
Docker container blj dir: "/app/biolockj"
- CONTAINER_ID_KEY - Static variable in class biolockj.util.DockerUtil
-
- containerizePath(String) - Static method in class biolockj.util.DockerUtil
-
If running in docker mode, convert this path to the form that can be used inside the docker container.
- containerizePath(File) - Static method in class biolockj.util.DockerUtil
-
- containsHn2ParserOutput(Collection<File>) - Static method in class biolockj.util.PathwayUtil
-
Check pipeline input contains Humann2Parser module output.
- convertRelativePath(String, File) - Static method in class biolockj.Config
-
Given a relative path (ie, one that starts with "."), get the absolute path---even when runnig in docker.
- convertWindowsPath(String) - Method in class biolockj.util.paths.CommonDockerMapper
-
- convertWindowsPathForDocker(String) - Static method in class biolockj.Config
-
- copyBatchOtuTableToOutputDir(File, Integer) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
-
The method returns 1 bash script line that will copy the batch
"otu_table.biom" from the batchDir to the output directory.
- copyDEseqScript() - Method in class biolockj.module.rnaseq.DESeq2
-
- copyEdgeRScript() - Method in class biolockj.module.rnaseq.EdgeR
-
- copyFileToPipelineRoot(File) - Static method in class biolockj.BioLockJ
-
Copy file to pipeline root directory.
- copyFromFile(File) - Static method in class biolockj.api.BuildDocs
-
- copyFromModuleResource(BioModule, String) - Static method in class biolockj.api.BuildDocs
-
- copyInputData() - Static method in class biolockj.BioLockJ
-
- copyInputFiles() - Static method in class biolockj.util.BioLockJUtil
-
Copy input files into an internal folder within the pipeline root direction named "input"
- copyTempOtuTableToOutputDir() - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier
-
The method returns 1 bash script line that will copy the batch
"otu_table.biom" from the batchDir to the output directory.
- countNumReads(File) - Static method in class biolockj.util.SeqUtil
-
Method counts number of reads in the given sequence file by counting the number of lines and dividing by the
number of lines/sample (fasta=2, fastq=4)
- createCmd() - Method in class biolockj.launch.DockerLaunchProcess
-
- createCmd() - Method in class biolockj.launch.JavaLaunchProcess
-
- createCmd() - Method in class biolockj.launch.LaunchProcess
-
- createFile(String) - Static method in class biolockj.util.BioLockJUtil
-
Used to save status files for modules and the pipeline.
- createModuleInstance(String) - Static method in class biolockj.util.ModuleUtil
-
Construct a BioModule based on its className to add it to the pipeline.
- createScript(ScriptModule, String, List<String>) - Static method in class biolockj.util.BashScriptBuilder
-
Create the script.