- HALT_PIPELINE - Static variable in class biolockj.util.ValidationUtil
-
Config
boolean property "validation.stopPipeline".
- handleBioLockJException(BioLockJException) - Static method in class biolockj.launch.Launcher
-
- handleEndLaunchException(EndLaunch) - Static method in class biolockj.launch.Launcher
-
- handleGeneralException(Exception) - Static method in class biolockj.launch.Launcher
-
- hasColumn(String) - Static method in class biolockj.util.MetaUtil
-
Check if columnName exists in the current metadata file.
- hasExecuted(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return TRUE if module has executed.
- hashCode() - Method in class biolockj.module.BioModuleImpl
-
- hashCode() - Method in class biolockj.node.JsonNode
-
- hashCode() - Method in class biolockj.node.ParsedSample
-
- hasMetaColToSampleIdMap() - Static method in class biolockj.util.MetaUtil
-
- hasNullOrEmptyVal(Collection<Object>) - Static method in class biolockj.util.BioLockJUtil
-
Check collection vals for null or empty toString() values
- hasPairedReads() - Static method in class biolockj.util.SeqUtil
-
- hasScripts() - Method in class biolockj.module.ScriptModuleImpl
-
Check if module produced any scripts
- hasScripts(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Check a BioModule for scripts to execute.
- hasStrictValidation(boolean) - Static method in class biolockj.util.ValidationUtil
-
Print a message (and return boolean) to indicate that this pipeline has validation enabled.
- hasValidBarcodes() - Static method in class biolockj.util.DemuxUtil
-
Check for the existance of the barcode column.
- Hello_Friends - Class in biolockj.module.hello_world
-
- Hello_Friends() - Constructor for class biolockj.module.hello_world.Hello_Friends
-
- Hello_World - Class in biolockj.module.hello_world
-
- Hello_World() - Constructor for class biolockj.module.hello_world.Hello_World
-
- HELP - Static variable in class biolockj.Constants
-
Argument to print help menu: "-help"
- HIER_COUNTS - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
- HIER_SUFFIX - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
-
- HIT_RATIO - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables
-
- HN2_DISABLE_GENE_FAMILIES - Static variable in class biolockj.Constants
-
Config
Boolean property: "humann2.disableGeneFamilies"
- HN2_DISABLE_PATH_ABUNDANCE - Static variable in class biolockj.Constants
-
Config
Boolean property: "humann2.disablePathAbundance"
- HN2_DISABLE_PATH_COVERAGE - Static variable in class biolockj.Constants
-
Config
Boolean property: "humann2.disablePathCoverage"
- HN2_GENE_FAM_SUM - Static variable in class biolockj.Constants
-
HumanN2 file suffix identifier for Gene Family Summary report: "geneFam"
- HN2_KEEP_UNINTEGRATED - Static variable in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
Config
Boolean property: "humann2.keepUnintegrated"
- HN2_KEEP_UNMAPPED - Static variable in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
Config
Boolean property: "humann2.keepUnmapped"
- HN2_NUCL_DB - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier
-
- HN2_PATH_ABUND_SUM - Static variable in class biolockj.Constants
-
HumanN2 file suffix identifier for Pathway Abundance Summary report: "pAbund"
- HN2_PATH_COVG_SUM - Static variable in class biolockj.Constants
-
HumanN2 file suffix identifier for Pathway Coverage Summary report: "pCovg"
- HN2_PROT_DB - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier
-
- HN2_TOTAL_PATH_COUNT - Static variable in class biolockj.Constants
-
HumanN2 meta column to store the total pathway count/sample: "Total_Pathways"
- HN2_UNIQUE_PATH_COUNT - Static variable in class biolockj.Constants
-
- HOME_DIR - Static variable in class biolockj.util.RuntimeParamUtil
-
Automatically added $HOME by biolockj/dockblj script: "-homeDir"
- HOST_EXE_PREFIX - Static variable in class biolockj.Constants
-
Prefix used in several
Config
String properties.
- howExciting() - Method in class biolockj.module.hello_world.Hello_Friends
-
- howExciting() - Method in class biolockj.module.hello_world.Step5
-
- howToLinkMetaWithFile - Static variable in exception biolockj.exception.MetadataException
-
- Humann2Classifier - Class in biolockj.module.classifier.wgs
-
This BioModule runs biobakery humann2 program to generate the HMP Unified Metabolic Analysis Network
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial
pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA
reads).
- Humann2Classifier() - Constructor for class biolockj.module.classifier.wgs.Humann2Classifier
-
- Humann2CountModule - Class in biolockj.module.report.humann2
-
This abstract superclass is extended by all other modules in this package.
Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites.
- Humann2CountModule() - Constructor for class biolockj.module.report.humann2.Humann2CountModule
-
- Humann2Parser - Class in biolockj.module.implicit.parser.wgs
-
This BioModule parses Humann2Classifier output reports to build standard OTU abundance tables.
Samples IDs are found in the column headers starting with the 2nd column.
The count type depends on the HumanN2 config properties.
- Humann2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Humann2Parser
-