Constants

java.lang.Object
- biolockj.Constants

```
public class Constants
extends Object
```
Single Java class to hold shared constant values referenced my multiple classes.

Field Summary

Fields
Modifier and Type	Field and Description
`static long`	`APP_START_TIME` Captures the application start time
`static String`	`ASSIGN_ALIAS` The key string to define an alias for an individual module: {@value
`static String`	`AWS_S3_XFER_TIMEOUT` `Config` Integer property: "aws.s3TransferTimeout"
`static String`	`BASH_PROFILE` Bash profile fo;e name: ".bash_profile"
`static String`	`BASH_RC` Bashrc file name: ".bashrc"
`static String`	`BLJ_COMPLETE` Name of the file created in the BioModule or "internal.pipelineDir" root directory to indicate execution was successful: "biolockjComplete"
`static String`	`BLJ_FAILED` Name of the file created in the "internal.pipelineDir" root directory to indicate fatal application errors halted execution: "biolockjFailed"
`static String`	`BLJ_MODULE_TAG` Set "#BioModule" tag in `Config` file to include in pipeline: "#BioModule" Example: #BioModule biolockj.module.ImportMetadata
`static String`	`BLJ_STARTED` Name of the file created in the BioModule root directory to indicate execution has started: "biolockjStarted"
`static String`	`BLJ_VERSION_PROP` `Config` property: "biolockj.version" "Property giving the biolockj version that was used to generate the config file."
`static String`	`BLJ_VERSION_PROP_DESC`
`static String`	`BLJ_WIKI` URL to the BioLockJ WIKI
`static String`	`CLASS` `Config` option for "report.taxonomyLevels": "class"
`static String`	`CLUSTER_HOST` `Config` "string" property: "cluster.host"
`static String`	`DEFAULT_MOD_DEMUX` `Config` property: "pipeline.defaultDemultiplexer"
`static String`	`DEFAULT_MOD_FASTA_CONV` `Config` property: "pipeline.defaultFastaConverter"
`static String`	`DEFAULT_MOD_SEQ_MERGER` `Config` property: "pipeline.defaultSeqMerger"
`static String`	`DEFAULT_STATS_MODULE` `Config` property: "pipeline.defaultStatsModule"
`static String`	`DELIM_SEP` In an otu string for multiple levels, each separated by "\|", each otu has a level prefix ending with "__"
`static String`	`DETACH_JAVA_MODULES` `Config` property: "pipeline.detachJavaModules"
`static String`	`DEVELOPER_NOTE` A prefix used for some messages.
`static String`	`DISABLE_ADD_IMPLICIT_MODULES` `Config` "boolean" property: "pipeline.disableAddImplicitModules"
`static String`	`DISABLE_PRE_REQ_MODULES` `Config` property: "pipeline.disableAddPreReqModules"
`static String`	`DOCKER_CONFIG_PATH` `Config` property: "${BLJ}/resources/config/default/docker.properties" Default path for an additional configuration file used for any pipeline run in docker.
`static String`	`DOCKER_EXE_PREFIX` Prefix used in several `Config` String properties.
`static String`	`DOMAIN` `Config` option for "report.taxonomyLevels": "domain"
`static String`	`DOWNLOAD_DIR` `Config` String property: "pipeline.downloadDir"
`static String`	`EXE_AWK` `Config` "executable" property: "exe.awk"
`static String`	`EXE_DOCKER` `Config` "executable" property: "exe.docker"
`static String`	`EXE_GZIP` `Config` "executable" property: "exe.gzip"
`static String`	`EXE_JAVA` `Config` "executable" property: "exe.java"
`static String`	`EXE_PREFIX` Prefix used in several `Config` String properties.
`static String`	`EXE_PYTHON` `Config` "executable" property: "exe.python"
`static String`	`EXE_RSCRIPT` `Config` "executable" property: "exe.Rscript"
`static String`	`FALSE` Boolean `Config` property value option: "N"
`static String`	`FAMILY` `Config` option for "report.taxonomyLevels": "family"
`static String`	`FASTA` File extension for fasta files = "fasta"
`static String`	`FASTQ` File extension for fastq files: "fastq"
`static String`	`GENUS` `Config` option for "report.taxonomyLevels": "genus"
`static String`	`GZIP_EXT` Gzip compressed file extension: ".gz"
`static String`	`HELP` Argument to print help menu: "-help"
`static String`	`HN2_DISABLE_GENE_FAMILIES` `Config` Boolean property: "humann2.disableGeneFamilies"
`static String`	`HN2_DISABLE_PATH_ABUNDANCE` `Config` Boolean property: "humann2.disablePathAbundance"
`static String`	`HN2_DISABLE_PATH_COVERAGE` `Config` Boolean property: "humann2.disablePathCoverage"
`static String`	`HN2_GENE_FAM_SUM` HumanN2 file suffix identifier for Gene Family Summary report: "geneFam"
`static String`	`HN2_PATH_ABUND_SUM` HumanN2 file suffix identifier for Pathway Abundance Summary report: "pAbund"
`static String`	`HN2_PATH_COVG_SUM` HumanN2 file suffix identifier for Pathway Coverage Summary report: "pCovg"
`static String`	`HN2_TOTAL_PATH_COUNT` HumanN2 meta column to store the total pathway count/sample: "Total_Pathways"
`static String`	`HN2_UNIQUE_PATH_COUNT` HumanN2 meta column to store the unique pathway count/sample: "Total_Pathways"
`static String`	`HOST_EXE_PREFIX` Prefix used in several `Config` String properties.
`static String`	`INDENT` Standard indent = 4 spaces.
`static String`	`INPUT_ALLOW_DUPS` `Config` boolean property:
`static String`	`INPUT_DIRS` `Config` List property: "input.dirPaths"
`static String`	`INPUT_FORWARD_READ_SUFFIX` `Config` String property: "input.suffixFw" Set file suffix used to identify forward reads in "input.dirPaths"
`static String`	`INPUT_IGNORE_FILES` `Config` List property: "input.ignoreFiles"
`static String`	`INPUT_REQUIRE_COMPLETE_PAIRS` `Config` Boolean property: "input.requireCompletePairs" "Require all sequence input files have matching paired reads"
`(package private) static String`	`INPUT_REQUIRE_COMPLETE_PAIRS_DESC`
`static String`	`INPUT_REVERSE_READ_SUFFIX` `Config` String property: "input.suffixRv" Set file suffix used to identify reverse reads in "input.dirPaths"
`static String`	`INPUT_TRIM_PREFIX` `Config` String property: "input.trimPrefix"
`static String`	`INPUT_TRIM_SUFFIX` `Config` String property: "input.trimSuffix"
`static String`	`INPUT_TYPES` `Config` List property: "pipeline.inputTypes"
`static String`	`INTERNAL_ALL_MODULES` Internal `Config` List property: "internal.allModules" List of all configured, implicit, and pre/post-requisite modules for the pipeline. Example: biolockj.module.ImportMetadata, etc.
`static String`	`INTERNAL_BLJ_MODULE` Internal `Config` List property: "internal.configModules" List of all project config modules.
`static String`	`INTERNAL_DEFAULT_CONFIG` Internal `Config` List property: "internal.defaultConfig" List of all nested default config files.
`static String`	`INTERNAL_IS_MULTI_LINE_SEQ` `Config` Internal Boolean property: "internal.isMultiLineSeq" Store TRUE if `SeqUtil` determines input sequences are multi-line format.
`static String`	`INTERNAL_MULTIPLEXED` `Config` Boolean property: "internal.multiplexed" Set to true if multiplexed reads are found, set by the application runtime code.
`static String`	`INTERNAL_PAIRED_READS` `Config` Boolean property: "internal.pairedReads" Set to true if paired reads are found, set by the application runtime code.
`static String`	`INTERNAL_PIPELINE_DIR` `Config` String property: "internal.pipelineDir" Stores the path of the pipeline root directory path set by the application runtime code.
`static String`	`INTERNAL_PIPELINE_ID` `Config` String property: "internal.pipelineInstanceId" The pipeline instance id is generally formed from the pipeline name, the date the pipeline started and sometimes an additional integer to ensure an unique folder name.
`static String`	`INTERNAL_PIPELINE_NAME` `Config` String property: "internal.pipelineName" Stores the name of the pipeline.
`static String`	`INTERNAL_PREFIX` Any `Config` property that starts with the "internal." prefix will not be included in the final MASTER properties file.
`static String`	`INTERNAL_SEQ_HEADER_CHAR` `Config` property: "internal.seqHeaderChar" The property holds the 1st character used in the sequence header for the given dataset
`static String`	`INTERNAL_SEQ_TYPE` `Config` Internal property: "internal.seqType" The sequence type requires either "fasta" or "fastq" System will auto-detect if not configured
`static String`	`JAR_ARG` Java runtime arg used to pass application jar path: "-jar"
`static String`	`LIMIT_DEBUG_CLASSES` `Config` property used to limit classes that log debug statements when "pipeline.logLevel"="Y" TODO: make this clearer.
`static String`	`LOG_EXT` BioLockJ log file extension: ".log"
`static String`	`LOG_LEVEL_PROPERTY` `Config` property used to set log sensitivity in log4j.properties log4j.rootLogger=${pipeline.logLevel}, file, stdout DEBUG - Log all messages INFO - Log info, warning and error messages WARN - Log warning and error messages ERROR - Log error messages only
`static String`	`LOG_SPACER` Spacer used to improve log file readability
`static String`	`MAIN_DOCKER_IMAGE` Docker image used for the BioLockJ head node.
`static String`	`MAIN_DOCKER_OWNER` Docker hub account that owns the .
`static String`	`markDownReturn` When writing mark down files, use this as a new line to start a new paragraph.
`static String`	`MASTER_PREFIX` Prefix added to the master Config file: "MASTER_"
`static String`	`MODULE_SEQ_PACKAGE` BioLockJ SEQ module package: "biolockj.module.seq"
`static String`	`MODULE_WGS_CLASSIFIER_PACKAGE` BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"
`static String`	`ORDER` `Config` option for "report.taxonomyLevels": "order"
`static String`	`OTU_COUNT` Included in the file name of each file output.
`static String`	`OTU_SEPARATOR` A pipe is used to separate each taxa "\|"
`static String`	`OTU_TABLE_PREFIX` QIIME OTU table prefix: "otu_table"
`static String`	`P_VAL_CUTOFF` `Config` property "r.pvalCutoff" defines the p-value cutoff for significance
`static String`	`PDF_EXT` BioLockJ PDF file extension: ".pdf"
`static String`	`PHYLUM` `Config` option for "report.taxonomyLevels": "phylum"
`static String`	`PIPELINE_COPY_FILES` `Config` property: "pipeline.copyInput"
`static String`	`PIPELINE_DEFAULT_PROPS` `Config` String property: "pipeline.defaultProps"
`static String`	`PIPELINE_DESC` `Config` property to allow a free-hand description to a pipeline: "pipeline.desc" TODO: needs to be implemented.
`static String`	`PIPELINE_ENV` `Config` String property: "pipeline.env"
`static String`	`PIPELINE_ENV_AWS` `Config` option for property: "pipeline.env" Used to indicate running as an Amazon web service: "aws"
`static String`	`PIPELINE_ENV_CLUSTER` `Config` option for property: "pipeline.env" Used to indicate running on the cluster: "cluster"
`static String`	`PIPELINE_ENV_LOCAL` `Config` option for property: "pipeline.env" Used to indicate running on a local machine (laptop, etc): "local"
`static String`	`PIPELINE_ENV_VARS` `Config` List property: "pipeline.env"
`static String`	`PIPELINE_ENV_VARS_DESC`
`static String`	`PIPELINE_LOCATION_KEY` Indicator for related programs (bash code, sheepdog_testing_suite) of the pipelines path: "Pipeline root directory: "
`static String`	`PIPELINE_NAME` `Config` property to assign a name to a pipeline: "pipeline.name" TODO: needs to be implemented.
`protected static String`	`PIPELINE_PRIVS` `Config` property: "pipeline.permissions"
`static String`	`PIPELINE_USE_EVARS` `Config` List property: "pipeline.useEnvVars" "when evaluating variables in the ${VAR} format, should environment variables be used. Regardless, priority is given to variable values defined in the config file."
`static String`	`PIPELINE_USE_EVARS_DESC`
`static String`	`PRECHECK_COMPLETE` Name of the file created in the BioModule root directory to indicate the precheck process encountered an error (if running in precheck mode): "precheckComplete"
`static String`	`PRECHECK_FAILED` Name of the file created in the BioModule root directory to indicate the precheck process has completed (if running in precheck mode): "precheckFailed"
`static String`	`PRECHECK_STARTED` Name of the file created in the BioModule root directory to indicate the precheck process has started (if running in precheck mode): "precheckStarted"
`static String`	`PROCESSED` File suffix appended to processed samples in the module output directory: "_reported.tsv"
`static String`	`PROJECT_DEFAULT_PROPS` `Config` String property: "project.defaultProps" Set file path of default property file.
`static String`	`PROJECT_DESC` `Config` property to assign a free-hand to a project: "project.description" TODO: needs to be implemented.
`static String`	`PROJECT_NAME` `Config` property to assign a name to a project: "project.name" TODO: needs to be implemented.
`static String`	`PROPS_EXT` BioLockJ properties file extension: ".properties"
`static String`	`QIIME` QIIME application: "qiime"
`static String`	`QIIME_ALPHA_DIVERSITY_METRICS` `Config` list property to calculate alpha diversity metrics. For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html "qiime.alphaMetrics"
`static String[]`	`QIIME_AMBIGUOUS_TAXA` Qiime may find ambiguous taxa identified in various formats in different databases.
`static String`	`QIIME_BARCODE_SEQ_COL` QIIME mapping file required 2nd column name
`static String`	`QIIME_DEMUX_COL` QIIME mapping column created by `BuildQiimeMapping` that stores the name of the original fasta file associated with the sample: "BioLockJFileName"
`static String`	`QIIME_DESC_COL` QIIME mapping file required name of last column
`static String`	`QIIME_LINKER_PRIMER_SEQ_COL` QIIME mapping file required 3rd column name
`static String`	`R_COLOR_BASE` `Config` property "r.colorBase"
`static String`	`R_COLOR_FILE` `Config` property "r.colorFile" gives the path to a tab-delimited file giving the color to use for each value of each metadata filed plotted.
`static String`	`R_COLOR_HIGHLIGHT` `Config` property "r.colorHighlight" defines the highlight label color
`static String`	`R_COLOR_PALETTE` `Config` property "r.colorPalette" defines the color palette for PDF plots
`static String`	`R_COLOR_POINT` `Config` property "r.colorPoint" defines the pch point colors for PDF plots
`static String`	`R_DEBUG` `Config` boolean property "r.debug" sets the debug log function enabled
`static String`	`R_EXT` File extension of BioLockJ generated R Scripts: ".R"
`static String`	`R_FUNCTION_LIB` This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"
`static String`	`R_INTERNAL_RUN_HN2` `Config` Boolean property to signal R scripts to build HumanN2 reports
`static String`	`R_MAIN_SCRIPT` This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"
`static String`	`R_PCH` `Config` property "r.pch" defines the plot point shape for PDF plots
`static String`	`R_RARE_OTU_THRESHOLD` `Config` Double property "r.rareOtuThreshold" defines number OTUs needed to includ in reports
`static String`	`R_SAVE_R_DATA` `Config` boolean property "r.saveRData" enables the .RData file to save.
`static String`	`R_TIMEOUT` `Config` property "r.timeout":
`static String`	`R_USE_UINQUE_COLORS`
`static String`	`RDP_THRESHOLD_SCORE` `Config` String property: "rdp.minThresholdScore" RdpParser will ignore OTU assignments below the threshold score (0-100)
`static String`	`REPORT_LOG_BASE` `Config` String property: "report.logBase" Required to be set to "e" or "10" to build log normalized reports.
`static String`	`REPORT_MIN_COUNT` `Config` Positive Integer property "report.minCount" defines the minimum table count allowed, if a count less that this value is found, it is set to 0.
`static String`	`REPORT_NUM_HITS` `Config` Boolean property: "report.numHits" If set to "Y", NUM_OTUS will be added to metadata file by `ParserModuleImpl` and included in R reports
`static String`	`REPORT_NUM_READS` `Config` Boolean property: "report.numReads" If set to "Y" and NUM_READS exists in metadata file, NUM_READS will be included in the R reports
`static String`	`REPORT_SAMPLE_CUTOFF` `Config` Positive Double property "report.scarceSampleCutoff" defines minimum percentage of data columns must be non-zero to keep the sample.
`static String`	`REPORT_SCARCE_CUTOFF` `Config` Positive Double property "report.scarceCountCutoff" defines minimum percentage of samples that must contain a count value for it to be kept.
`static String`	`REPORT_TAXONOMY_LEVELS` `Config` List property: "report.taxonomyLevels" This property drives a lot of BioLockJ functionality and determines which taxonomy-levels are reported.
`static String`	`REPORT_UNCLASSIFIED_TAXA` `Config` Boolean property: "report.unclassifiedTaxa"
`static String`	`RETURN` Return character: backslash-n
`static String`	`RM_TEMP_FILES` `Config` property: "pipeline.deleteTempFiles"
`static String`	`RSCRIPT` Rscript exe commmand.
`static String`	`SCRIPT_DEFAULT_HEADER` `Config` List property: "script.defaultHeader" "Store default script header for MAIN script and locally run WORKER scripts."
`static String`	`SCRIPT_DEFAULT_HEADER_DESC`
`static String`	`SCRIPT_DELAY_FOR_FILE_UPDATES` `Config` List property: "script.fileRefreshDelay" In some cases, especially with virtualization, there may be delays between before the program is able to register file system changes made by another container/node/host.
`static String`	`SCRIPT_DIR` Name of the script sub-directory: "script"
`static String`	`SCRIPT_FAILURES` File suffix appended to failed scripts: "Failures"
`static String`	`SCRIPT_NUM_THREADS` `Config` Integer property: "script.numThreads" "Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter."
`static String`	`SCRIPT_NUM_THREADS_DESC`
`static String`	`SCRIPT_NUM_WORKERS` `Config` Integer property: "script.numWorkers" "Set number of samples to process per script (if parallel processing)"
`static String`	`SCRIPT_NUM_WORKERS_DESC`
`static String`	`SCRIPT_PERMISSIONS` `Config` String property: "script.permissions" "Used as chmod permission parameter (ex: 774)"
`static String`	`SCRIPT_PERMISSIONS_DESC`
`static String`	`SCRIPT_STARTED` File suffix appended to started script: "Started"
`static String`	`SCRIPT_SUCCESS` File suffix appended to successful scripts: "Success"
`static String`	`SCRIPT_TIMEOUT` `Config` Integer property: "script.timeout" "Sets # of minutes before worker scripts times out."
`static String`	`SCRIPT_TIMEOUT_DESC`
`static String`	`SET_SEED` `Config` property "pipeline.setSeed"
`static String`	`SH_EXT` BioLockJ shell script file extension: ".sh"
`static String`	`SPECIES` `Config` option for "report.taxonomyLevels": "species"
`static String`	`STANDARD_CONFIG_PATH` Default `Config` imported for all pipelines (if file exists)
`static String`	`STATUS_MARK_KEY` Key used in standard err messages indicating that this line should be shown to the user.
`static String`	`STATUS_START_KEY` Key used in standard err messages indicating that this line should be shown to the user.
`static String`	`TAB_DELIM` BioLockJ tab character: "\t"
`static String`	`TRUE` Boolean `Config` property value option: "Y"
`static String`	`TSV_EXT` BioLockJ tab delimited text file extension: ".tsv"
`static String`	`TXT_EXT` BioLockJ standard text file extension: ".txt"
`static String`	`UNCLASSIFIED` Unclassified taxa prefix: "Unclassified"
`static String`	`UNVERIFIED_PROPS_FILE`
`static String`	`USER_PROFILE` `Config` File property: "pipeline.userProfile"
`static String`	`VALIDATION_ENABLED` String used by sheepdog_testing_suite to assert that validation is enabled: "This pipeline has validation enabled.".
`static String`	`VERSION` BioLockJ main() runtime arg used to print version info: "-version"
`static String`	`YEAR_AND_OWNER` The year and owner of this program as of most recent development.

Constructor Summary

Constructors
Constructor and Description

Constants()

Constructors
Constructor and Description
`Constants()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`(package private) static void`	`registerProps()` Register properties with the Properties class for API access.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - APP_START_TIME
```
public static final long APP_START_TIME
```
    Captures the application start time
  - ASSIGN_ALIAS
```
public static final String ASSIGN_ALIAS
```
    The key string to define an alias for an individual module: {@value
    
    See Also:
    
    Constant Field Values
  - AWS_S3_XFER_TIMEOUT
```
public static final String AWS_S3_XFER_TIMEOUT
```
    Config Integer property: "aws.s3TransferTimeout"
    
    See Also:
    
    Constant Field Values
  - BASH_PROFILE
```
public static final String BASH_PROFILE
```
    Bash profile fo;e name: ".bash_profile"
    
    See Also:
    
    Constant Field Values
  - BASH_RC
```
public static final String BASH_RC
```
    Bashrc file name: ".bashrc"
    
    See Also:
    
    Constant Field Values
  - BLJ_COMPLETE
```
public static final String BLJ_COMPLETE
```
    Name of the file created in the BioModule or "internal.pipelineDir" root directory to indicate execution was successful: "biolockjComplete"
    
    See Also:
    
    Constant Field Values
  - BLJ_FAILED
```
public static final String BLJ_FAILED
```
    Name of the file created in the "internal.pipelineDir" root directory to indicate fatal application errors halted execution: "biolockjFailed"
    
    See Also:
    
    Constant Field Values
  - BLJ_MODULE_TAG
```
public static final String BLJ_MODULE_TAG
```
    Set "#BioModule" tag in Config file to include in pipeline: "#BioModule"
    Example: #BioModule biolockj.module.ImportMetadata
    
    See Also:
    
    Constant Field Values
  - BLJ_STARTED
```
public static final String BLJ_STARTED
```
    Name of the file created in the BioModule root directory to indicate execution has started: "biolockjStarted"
    
    See Also:
    
    Constant Field Values
  - BLJ_VERSION_PROP
```
public static final String BLJ_VERSION_PROP
```
    Config property: "biolockj.version"
    "Property giving the biolockj version that was used to generate the config file."
    
    See Also:
    
    Constant Field Values
  - BLJ_VERSION_PROP_DESC
```
public static final String BLJ_VERSION_PROP_DESC
```
    See Also:
    
    Constant Field Values
  - BLJ_WIKI
```
public static final String BLJ_WIKI
```
    URL to the BioLockJ WIKI
    
    See Also:
    
    Constant Field Values
  - CLASS
```
public static final String CLASS
```
    Config option for "report.taxonomyLevels": "class"
    
    See Also:
    
    Constant Field Values
  - CLUSTER_HOST
```
public static final String CLUSTER_HOST
```
    Config "string" property: "cluster.host"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MOD_DEMUX
```
public static final String DEFAULT_MOD_DEMUX
```
    Config property: "pipeline.defaultDemultiplexer"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MOD_FASTA_CONV
```
public static final String DEFAULT_MOD_FASTA_CONV
```
    Config property: "pipeline.defaultFastaConverter"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MOD_SEQ_MERGER
```
public static final String DEFAULT_MOD_SEQ_MERGER
```
    Config property: "pipeline.defaultSeqMerger"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_STATS_MODULE
```
public static final String DEFAULT_STATS_MODULE
```
    Config property: "pipeline.defaultStatsModule"
    
    See Also:
    
    Constant Field Values
  - DELIM_SEP
```
public static final String DELIM_SEP
```
    In an otu string for multiple levels, each separated by "|", each otu has a level prefix ending with "__"
    
    See Also:
    
    Constant Field Values
  - DETACH_JAVA_MODULES
```
public static final String DETACH_JAVA_MODULES
```
    Config property: "pipeline.detachJavaModules"
    
    See Also:
    
    Constant Field Values
  - DEVELOPER_NOTE
```
public static final String DEVELOPER_NOTE
```
    A prefix used for some messages. These are messages to alert a developer about changes that may be needed. These notes should only appear in debug mode (Log.debug()).
    
    See Also:
    
    Constant Field Values
  - DISABLE_ADD_IMPLICIT_MODULES
```
public static final String DISABLE_ADD_IMPLICIT_MODULES
```
    Config "boolean" property: "pipeline.disableAddImplicitModules"
    
    See Also:
    
    Constant Field Values
  - DISABLE_PRE_REQ_MODULES
```
public static final String DISABLE_PRE_REQ_MODULES
```
    Config property: "pipeline.disableAddPreReqModules"
    
    See Also:
    
    Constant Field Values
  - DOCKER_CONFIG_PATH
```
public static final String DOCKER_CONFIG_PATH
```
    Config property: "${BLJ}/resources/config/default/docker.properties" Default path for an additional configuration file used for any pipeline run in docker.
    
    See Also:
    
    Constant Field Values
  - DOCKER_EXE_PREFIX
```
public static final String DOCKER_EXE_PREFIX
```
    Prefix used in several Config String properties. "dockerExe."
    
    See Also:
    
    EXE_PREFIX, Constant Field Values
  - DOMAIN
```
public static final String DOMAIN
```
    Config option for "report.taxonomyLevels": "domain"
    
    See Also:
    
    Constant Field Values
  - DOWNLOAD_DIR
```
public static final String DOWNLOAD_DIR
```
    Config String property: "pipeline.downloadDir"
    
    See Also:
    
    Constant Field Values
  - EXE_PREFIX
```
public static final String EXE_PREFIX
```
    Prefix used in several Config String properties. "exe."
    These properties are used to give the path to executables. Unlike most file path properties, they are not converted from host-path style when using a docker container; thus, an ""exe."" property can be used to specify an executable within a docker container. In contrast, the "hostExe." prefix is used the same way, but it is translated to allow an in-container script to use the host file path specified.
    
    See Also:
    
    Constant Field Values
  - EXE_AWK
```
public static final String EXE_AWK
```
    Config "executable" property: "exe.awk"
    
    See Also:
    
    Constant Field Values
  - EXE_DOCKER
```
public static final String EXE_DOCKER
```
    Config "executable" property: "exe.docker"
    
    See Also:
    
    Constant Field Values
  - EXE_GZIP
```
public static final String EXE_GZIP
```
    Config "executable" property: "exe.gzip"
    
    See Also:
    
    Constant Field Values
  - EXE_JAVA
```
public static final String EXE_JAVA
```
    Config "executable" property: "exe.java"
    
    See Also:
    
    Constant Field Values
  - EXE_PYTHON
```
public static final String EXE_PYTHON
```
    Config "executable" property: "exe.python"
    
    See Also:
    
    Constant Field Values
  - EXE_RSCRIPT
```
public static final String EXE_RSCRIPT
```
    Config "executable" property: "exe.Rscript"
    
    See Also:
    
    Constant Field Values
  - FALSE
```
public static final String FALSE
```
    Boolean Config property value option: "N"
    
    See Also:
    
    Constant Field Values
  - FAMILY
```
public static final String FAMILY
```
    Config option for "report.taxonomyLevels": "family"
    
    See Also:
    
    Constant Field Values
  - FASTA
```
public static final String FASTA
```
    File extension for fasta files = "fasta"
    
    See Also:
    
    Constant Field Values
  - FASTQ
```
public static final String FASTQ
```
    File extension for fastq files: "fastq"
    
    See Also:
    
    Constant Field Values
  - GENUS
```
public static final String GENUS
```
    Config option for "report.taxonomyLevels": "genus"
    
    See Also:
    
    Constant Field Values
  - GZIP_EXT
```
public static final String GZIP_EXT
```
    Gzip compressed file extension: ".gz"
    
    See Also:
    
    Constant Field Values
  - HELP
```
public static final String HELP
```
    Argument to print help menu: "-help"
    
    See Also:
    
    Constant Field Values
  - HOST_EXE_PREFIX
```
public static final String HOST_EXE_PREFIX
```
    Prefix used in several Config String properties. "hostExe."
    
    See Also:
    
    EXE_PREFIX, Constant Field Values
  - HN2_DISABLE_GENE_FAMILIES
```
public static final String HN2_DISABLE_GENE_FAMILIES
```
    Config Boolean property: "humann2.disableGeneFamilies"
    
    See Also:
    
    Constant Field Values
  - HN2_DISABLE_PATH_ABUNDANCE
```
public static final String HN2_DISABLE_PATH_ABUNDANCE
```
    Config Boolean property: "humann2.disablePathAbundance"
    
    See Also:
    
    Constant Field Values
  - HN2_DISABLE_PATH_COVERAGE
```
public static final String HN2_DISABLE_PATH_COVERAGE
```
    Config Boolean property: "humann2.disablePathCoverage"
    
    See Also:
    
    Constant Field Values
  - HN2_GENE_FAM_SUM
```
public static final String HN2_GENE_FAM_SUM
```
    HumanN2 file suffix identifier for Gene Family Summary report: "geneFam"
    
    See Also:
    
    Constant Field Values
  - HN2_PATH_ABUND_SUM
```
public static final String HN2_PATH_ABUND_SUM
```
    HumanN2 file suffix identifier for Pathway Abundance Summary report: "pAbund"
    
    See Also:
    
    Constant Field Values
  - HN2_PATH_COVG_SUM
```
public static final String HN2_PATH_COVG_SUM
```
    HumanN2 file suffix identifier for Pathway Coverage Summary report: "pCovg"
    
    See Also:
    
    Constant Field Values
  - HN2_TOTAL_PATH_COUNT
```
public static final String HN2_TOTAL_PATH_COUNT
```
    HumanN2 meta column to store the total pathway count/sample: "Total_Pathways"
    
    See Also:
    
    Constant Field Values
  - HN2_UNIQUE_PATH_COUNT
```
public static final String HN2_UNIQUE_PATH_COUNT
```
    HumanN2 meta column to store the unique pathway count/sample: "Total_Pathways"
    
    See Also:
    
    Constant Field Values
  - INDENT
```
public static final String INDENT
```
    Standard indent = 4 spaces.
    
    See Also:
    
    Constant Field Values
  - INPUT_ALLOW_DUPS
```
public static final String INPUT_ALLOW_DUPS
```
    Config boolean property:
    
    See Also:
    
    Constant Field Values
  - INPUT_DIRS
```
public static final String INPUT_DIRS
```
    Config List property: "input.dirPaths"
    
    See Also:
    
    Constant Field Values
  - INPUT_FORWARD_READ_SUFFIX
```
public static final String INPUT_FORWARD_READ_SUFFIX
```
    Config String property: "input.suffixFw"
    Set file suffix used to identify forward reads in "input.dirPaths"
    
    See Also:
    
    Constant Field Values
  - INPUT_IGNORE_FILES
```
public static final String INPUT_IGNORE_FILES
```
    Config List property: "input.ignoreFiles"
    
    See Also:
    
    Constant Field Values
  - INPUT_REQUIRE_COMPLETE_PAIRS
```
public static final String INPUT_REQUIRE_COMPLETE_PAIRS
```
    Config Boolean property: "input.requireCompletePairs"
    "Require all sequence input files have matching paired reads"
    
    See Also:
    
    Constant Field Values
  - INPUT_REQUIRE_COMPLETE_PAIRS_DESC
```
static final String INPUT_REQUIRE_COMPLETE_PAIRS_DESC
```
    See Also:
    
    Constant Field Values
  - INPUT_REVERSE_READ_SUFFIX
```
public static final String INPUT_REVERSE_READ_SUFFIX
```
    Config String property: "input.suffixRv"
    Set file suffix used to identify reverse reads in "input.dirPaths"
    
    See Also:
    
    Constant Field Values
  - INPUT_TRIM_PREFIX
```
public static final String INPUT_TRIM_PREFIX
```
    Config String property: "input.trimPrefix"
    
    See Also:
    
    Constant Field Values
  - INPUT_TRIM_SUFFIX
```
public static final String INPUT_TRIM_SUFFIX
```
    Config String property: "input.trimSuffix"
    
    See Also:
    
    Constant Field Values
  - INPUT_TYPES
```
public static final String INPUT_TYPES
```
    Config List property: "pipeline.inputTypes"
    
    See Also:
    
    Constant Field Values
  - INTERNAL_PREFIX
```
public static final String INTERNAL_PREFIX
```
    Any Config property that starts with the "internal." prefix will not be included in the final MASTER properties file.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_ALL_MODULES
```
public static final String INTERNAL_ALL_MODULES
```
    Internal Config List property: "internal.allModules"
    List of all configured, implicit, and pre/post-requisite modules for the pipeline.
    Example: biolockj.module.ImportMetadata, etc.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_BLJ_MODULE
```
public static final String INTERNAL_BLJ_MODULE
```
    Internal Config List property: "internal.configModules"
    List of all project config modules.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_DEFAULT_CONFIG
```
public static final String INTERNAL_DEFAULT_CONFIG
```
    Internal Config List property: "internal.defaultConfig"
    List of all nested default config files.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_IS_MULTI_LINE_SEQ
```
public static final String INTERNAL_IS_MULTI_LINE_SEQ
```
    Config Internal Boolean property: "internal.isMultiLineSeq"
    Store TRUE if SeqUtil determines input sequences are multi-line format.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_MULTIPLEXED
```
public static final String INTERNAL_MULTIPLEXED
```
    Config Boolean property: "internal.multiplexed"
    Set to true if multiplexed reads are found, set by the application runtime code.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_PAIRED_READS
```
public static final String INTERNAL_PAIRED_READS
```
    Config Boolean property: "internal.pairedReads"
    Set to true if paired reads are found, set by the application runtime code.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_PIPELINE_DIR
```
public static final String INTERNAL_PIPELINE_DIR
```
    Config String property: "internal.pipelineDir"
    Stores the path of the pipeline root directory path set by the application runtime code.
    
    See Also:
    
    Constant Field Values
  - INTERNAL_PIPELINE_NAME
```
public static final String INTERNAL_PIPELINE_NAME
```
    Config String property: "internal.pipelineName"
    Stores the name of the pipeline. This is distinct from the pipeline instance id, see
    
    See Also:
    
    Constant Field Values
  - INTERNAL_PIPELINE_ID
```
public static final String INTERNAL_PIPELINE_ID
```
    Config String property: "internal.pipelineInstanceId"
    The pipeline instance id is generally formed from the pipeline name, the date the pipeline started and sometimes an additional integer to ensure an unique folder name. The pipeline instance id is used as the folder name for the pipeline. The master properties file is named: + instance id +
    
    See Also:
    
    Constant Field Values
  - INTERNAL_SEQ_HEADER_CHAR
```
public static final String INTERNAL_SEQ_HEADER_CHAR
```
    Config property: "internal.seqHeaderChar"
    The property holds the 1st character used in the sequence header for the given dataset
    
    See Also:
    
    Constant Field Values
  - INTERNAL_SEQ_TYPE
```
public static final String INTERNAL_SEQ_TYPE
```
    Config Internal property: "internal.seqType"
    The sequence type requires either "fasta" or "fastq"
    System will auto-detect if not configured
    
    See Also:
    
    Constant Field Values
  - JAR_ARG
```
public static final String JAR_ARG
```
    Java runtime arg used to pass application jar path: "-jar"
    
    See Also:
    
    Constant Field Values
  - LIMIT_DEBUG_CLASSES
```
public static final String LIMIT_DEBUG_CLASSES
```
    Config property used to limit classes that log debug statements when "pipeline.logLevel"="Y" TODO: make this clearer. Are these the classes that will log debug, or the classes that will be 'limited' ?
    
    See Also:
    
    Constant Field Values
  - LOG_EXT
```
public static final String LOG_EXT
```
    BioLockJ log file extension: ".log"
    
    See Also:
    
    Constant Field Values
  - LOG_LEVEL_PROPERTY
```
public static final String LOG_LEVEL_PROPERTY
```
    Config property used to set log sensitivity in log4j.properties
    log4j.rootLogger=${pipeline.logLevel}, file, stdout
    1. DEBUG - Log all messages
    2. INFO - Log info, warning and error messages
    3. WARN - Log warning and error messages
    4. ERROR - Log error messages only
    See Also:
    
    Constant Field Values
  - LOG_SPACER
```
public static final String LOG_SPACER
```
    Spacer used to improve log file readability
    
    See Also:
    
    Constant Field Values
  - MAIN_DOCKER_IMAGE
```
public static final String MAIN_DOCKER_IMAGE
```
    Docker image used for the BioLockJ head node. Also used as a simple default for some modules.
    
    See Also:
    
    Constant Field Values
  - MAIN_DOCKER_OWNER
```
public static final String MAIN_DOCKER_OWNER
```
    Docker hub account that owns the . Also used as a simple default for some modules.
    
    See Also:
    
    Constant Field Values
  - markDownReturn
```
public static final String markDownReturn
```
    When writing mark down files, use this as a new line to start a new paragraph.
  - MASTER_PREFIX
```
public static final String MASTER_PREFIX
```
    Prefix added to the master Config file: "MASTER_"
    
    See Also:
    
    Constant Field Values
  - MODULE_SEQ_PACKAGE
```
public static final String MODULE_SEQ_PACKAGE
```
    BioLockJ SEQ module package: "biolockj.module.seq"
    
    See Also:
    
    Constant Field Values
  - MODULE_WGS_CLASSIFIER_PACKAGE
```
public static final String MODULE_WGS_CLASSIFIER_PACKAGE
```
    BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"
    
    See Also:
    
    Constant Field Values
  - ORDER
```
public static final String ORDER
```
    Config option for "report.taxonomyLevels": "order"
    
    See Also:
    
    Constant Field Values
  - OTU_COUNT
```
public static final String OTU_COUNT
```
    Included in the file name of each file output. One file per sample is output by the ParserModule.
    
    See Also:
    
    Constant Field Values
  - OTU_SEPARATOR
```
public static final String OTU_SEPARATOR
```
    A pipe is used to separate each taxa "|"
    
    See Also:
    
    Constant Field Values
  - OTU_TABLE_PREFIX
```
public static final String OTU_TABLE_PREFIX
```
    QIIME OTU table prefix: "otu_table"
    
    See Also:
    
    Constant Field Values
  - PDF_EXT
```
public static final String PDF_EXT
```
    BioLockJ PDF file extension: ".pdf"
    
    See Also:
    
    Constant Field Values
  - PHYLUM
```
public static final String PHYLUM
```
    Config option for "report.taxonomyLevels": "phylum"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_COPY_FILES
```
public static final String PIPELINE_COPY_FILES
```
    Config property: "pipeline.copyInput"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_DEFAULT_PROPS
```
public static final String PIPELINE_DEFAULT_PROPS
```
    Config String property: "pipeline.defaultProps"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_DESC
```
public static final String PIPELINE_DESC
```
    Config property to allow a free-hand description to a pipeline: "pipeline.desc" TODO: needs to be implemented.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV
```
public static final String PIPELINE_ENV
```
    Config String property: "pipeline.env"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV_VARS
```
public static final String PIPELINE_ENV_VARS
```
    Config List property: "pipeline.env"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV_VARS_DESC
```
public static final String PIPELINE_ENV_VARS_DESC
```
    See Also:
    
    Constant Field Values
  - PIPELINE_USE_EVARS
```
public static final String PIPELINE_USE_EVARS
```
    Config List property: "pipeline.useEnvVars"
    "when evaluating variables in the ${VAR} format, should environment variables be used. Regardless, priority is given to variable values defined in the config file."
    
    See Also:
    
    Constant Field Values
  - PIPELINE_USE_EVARS_DESC
```
public static final String PIPELINE_USE_EVARS_DESC
```
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV_AWS
```
public static final String PIPELINE_ENV_AWS
```
    Config option for property: "pipeline.env"
    Used to indicate running as an Amazon web service: "aws"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV_CLUSTER
```
public static final String PIPELINE_ENV_CLUSTER
```
    Config option for property: "pipeline.env"
    Used to indicate running on the cluster: "cluster"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_ENV_LOCAL
```
public static final String PIPELINE_ENV_LOCAL
```
    Config option for property: "pipeline.env"
    Used to indicate running on a local machine (laptop, etc): "local"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_LOCATION_KEY
```
public static final String PIPELINE_LOCATION_KEY
```
    Indicator for related programs (bash code, sheepdog_testing_suite) of the pipelines path: "Pipeline root directory: "
    
    See Also:
    
    Constant Field Values
  - PIPELINE_NAME
```
public static final String PIPELINE_NAME
```
    Config property to assign a name to a pipeline: "pipeline.name" TODO: needs to be implemented.
    
    See Also:
    
    Constant Field Values
  - PIPELINE_PRIVS
```
protected static final String PIPELINE_PRIVS
```
    Config property: "pipeline.permissions"
    
    See Also:
    
    Constant Field Values
  - PRECHECK_COMPLETE
```
public static final String PRECHECK_COMPLETE
```
    Name of the file created in the BioModule root directory to indicate the precheck process encountered an error (if running in precheck mode): "precheckComplete"
    
    See Also:
    
    Constant Field Values
  - PRECHECK_FAILED
```
public static final String PRECHECK_FAILED
```
    Name of the file created in the BioModule root directory to indicate the precheck process has completed (if running in precheck mode): "precheckFailed"
    
    See Also:
    
    Constant Field Values
  - PRECHECK_STARTED
```
public static final String PRECHECK_STARTED
```
    Name of the file created in the BioModule root directory to indicate the precheck process has started (if running in precheck mode): "precheckStarted"
    
    See Also:
    
    Constant Field Values
  - PROCESSED
```
public static final String PROCESSED
```
    File suffix appended to processed samples in the module output directory: "_reported.tsv"
    
    See Also:
    
    Constant Field Values
  - PROJECT_DEFAULT_PROPS
```
public static final String PROJECT_DEFAULT_PROPS
```
    Config String property: "project.defaultProps"
    Set file path of default property file. Nested default properties are supported (so the default property file can also have a default, and so on).
    
    See Also:
    
    Constant Field Values
  - PROJECT_DESC
```
public static final String PROJECT_DESC
```
    Config property to assign a free-hand to a project: "project.description" TODO: needs to be implemented.
    
    See Also:
    
    Constant Field Values
  - PROJECT_NAME
```
public static final String PROJECT_NAME
```
    Config property to assign a name to a project: "project.name" TODO: needs to be implemented.
    
    See Also:
    
    Constant Field Values
  - PROPS_EXT
```
public static final String PROPS_EXT
```
    BioLockJ properties file extension: ".properties"
    
    See Also:
    
    Constant Field Values
  - QIIME
```
public static final String QIIME
```
    QIIME application: "qiime"
    
    See Also:
    
    Constant Field Values
  - QIIME_ALPHA_DIVERSITY_METRICS
```
public static final String QIIME_ALPHA_DIVERSITY_METRICS
```
    Config list property to calculate alpha diversity metrics.
    For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html
    "qiime.alphaMetrics"
    
    See Also:
    
    Constant Field Values
  - QIIME_AMBIGUOUS_TAXA
```
public static final String[] QIIME_AMBIGUOUS_TAXA
```
    Qiime may find ambiguous taxa identified in various formats in different databases. The following accounts for Green Genes 13.8 and Silva 132: "Ambiguous_taxa", "Other", "Unassigned"
  - QIIME_BARCODE_SEQ_COL
```
public static final String QIIME_BARCODE_SEQ_COL
```
    QIIME mapping file required 2nd column name
    
    See Also:
    
    Constant Field Values
  - QIIME_DEMUX_COL
```
public static final String QIIME_DEMUX_COL
```
    QIIME mapping column created by BuildQiimeMapping that stores the name of the original fasta file associated with the sample: "BioLockJFileName"
    
    See Also:
    
    Constant Field Values
  - QIIME_DESC_COL
```
public static final String QIIME_DESC_COL
```
    QIIME mapping file required name of last column
    
    See Also:
    
    Constant Field Values
  - QIIME_LINKER_PRIMER_SEQ_COL
```
public static final String QIIME_LINKER_PRIMER_SEQ_COL
```
    QIIME mapping file required 3rd column name
    
    See Also:
    
    Constant Field Values
  - R_EXT
```
public static final String R_EXT
```
    File extension of BioLockJ generated R Scripts: ".R"
    
    See Also:
    
    Constant Field Values
  - P_VAL_CUTOFF
```
public static final String P_VAL_CUTOFF
```
    Config property "r.pvalCutoff" defines the p-value cutoff for significance
    
    See Also:
    
    Constant Field Values
  - R_COLOR_BASE
```
public static final String R_COLOR_BASE
```
    Config property "r.colorBase"
    
    See Also:
    
    Constant Field Values
  - R_COLOR_FILE
```
public static final String R_COLOR_FILE
```
    Config property "r.colorFile" gives the path to a tab-delimited file giving the color to use for each value of each metadata filed plotted.
    
    See Also:
    
    Constant Field Values
  - R_COLOR_HIGHLIGHT
```
public static final String R_COLOR_HIGHLIGHT
```
    Config property "r.colorHighlight" defines the highlight label color
    
    See Also:
    
    Constant Field Values
  - R_COLOR_PALETTE
```
public static final String R_COLOR_PALETTE
```
    Config property "r.colorPalette" defines the color palette for PDF plots
    
    See Also:
    
    Constant Field Values
  - R_COLOR_POINT
```
public static final String R_COLOR_POINT
```
    Config property "r.colorPoint" defines the pch point colors for PDF plots
    
    See Also:
    
    Constant Field Values
  - R_DEBUG
```
public static final String R_DEBUG
```
    Config boolean property "r.debug" sets the debug log function enabled
    
    See Also:
    
    Constant Field Values
  - R_FUNCTION_LIB
```
public static final String R_FUNCTION_LIB
```
    This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"
    
    See Also:
    
    Constant Field Values
  - R_MAIN_SCRIPT
```
public static final String R_MAIN_SCRIPT
```
    This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"
    
    See Also:
    
    Constant Field Values
  - R_PCH
```
public static final String R_PCH
```
    Config property "r.pch" defines the plot point shape for PDF plots
    
    See Also:
    
    Constant Field Values
  - R_RARE_OTU_THRESHOLD
```
public static final String R_RARE_OTU_THRESHOLD
```
    Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in reports
    
    See Also:
    
    Constant Field Values
  - R_SAVE_R_DATA
```
public static final String R_SAVE_R_DATA
```
    Config boolean property "r.saveRData" enables the .RData file to save.
    
    See Also:
    
    Constant Field Values
  - R_USE_UINQUE_COLORS
```
public static final String R_USE_UINQUE_COLORS
```
    See Also:
    
    Constant Field Values
  - R_TIMEOUT
```
public static final String R_TIMEOUT
```
    Config property "r.timeout":
    
    See Also:
    
    Constant Field Values
  - R_INTERNAL_RUN_HN2
```
public static final String R_INTERNAL_RUN_HN2
```
    Config Boolean property to signal R scripts to build HumanN2 reports
    
    See Also:
    
    Constant Field Values
  - RDP_THRESHOLD_SCORE
```
public static final String RDP_THRESHOLD_SCORE
```
    Config String property: "rdp.minThresholdScore"
    RdpParser will ignore OTU assignments below the threshold score (0-100)
    
    See Also:
    
    Constant Field Values
  - REPORT_LOG_BASE
```
public static final String REPORT_LOG_BASE
```
    Config String property: "report.logBase"
    Required to be set to "e" or "10" to build log normalized reports.
    
    See Also:
    
    Constant Field Values
  - REPORT_MIN_COUNT
```
public static final String REPORT_MIN_COUNT
```
    Config Positive Integer property "report.minCount" defines the minimum table count allowed, if a count less that this value is found, it is set to 0.
    
    See Also:
    
    Constant Field Values
  - REPORT_NUM_HITS
```
public static final String REPORT_NUM_HITS
```
    Config Boolean property: "report.numHits"
    If set to "Y", NUM_OTUS will be added to metadata file by ParserModuleImpl and included in R reports
    
    See Also:
    
    Constant Field Values
  - REPORT_NUM_READS
```
public static final String REPORT_NUM_READS
```
    Config Boolean property: "report.numReads"
    If set to "Y" and NUM_READS exists in metadata file, NUM_READS will be included in the R reports
    
    See Also:
    
    Constant Field Values
  - REPORT_SAMPLE_CUTOFF
```
public static final String REPORT_SAMPLE_CUTOFF
```
    Config Positive Double property "report.scarceSampleCutoff" defines minimum percentage of data columns must be non-zero to keep the sample.
    
    See Also:
    
    Constant Field Values
  - REPORT_SCARCE_CUTOFF
```
public static final String REPORT_SCARCE_CUTOFF
```
    Config Positive Double property "report.scarceCountCutoff" defines minimum percentage of samples that must contain a count value for it to be kept.
    
    See Also:
    
    Constant Field Values
  - REPORT_TAXONOMY_LEVELS
```
public static final String REPORT_TAXONOMY_LEVELS
```
    Config List property: "report.taxonomyLevels"
    This property drives a lot of BioLockJ functionality and determines which taxonomy-levels are reported. Note, some classifiers do not identify "species" level OTUs.
    Options = "domain", "phylum", "class", "order", "family", "genus", "species"
    
    See Also:
    
    Constant Field Values
  - REPORT_UNCLASSIFIED_TAXA
```
public static final String REPORT_UNCLASSIFIED_TAXA
```
    Config Boolean property: "report.unclassifiedTaxa"
    
    See Also:
    
    Constant Field Values
  - RETURN
```
public static final String RETURN
```
    Return character: *backslash-n*
    
    See Also:
    
    Constant Field Values
  - RM_TEMP_FILES
```
public static final String RM_TEMP_FILES
```
    Config property: "pipeline.deleteTempFiles"
    
    See Also:
    
    Constant Field Values
  - RSCRIPT
```
public static final String RSCRIPT
```
    Rscript exe commmand.
    
    See Also:
    
    Constant Field Values
  - SCRIPT_DEFAULT_HEADER
```
public static final String SCRIPT_DEFAULT_HEADER
```
    Config List property: "script.defaultHeader"
    "Store default script header for MAIN script and locally run WORKER scripts."
    
    See Also:
    
    Constant Field Values
  - SCRIPT_DEFAULT_HEADER_DESC
```
public static final String SCRIPT_DEFAULT_HEADER_DESC
```
    See Also:
    
    Constant Field Values
  - SCRIPT_DELAY_FOR_FILE_UPDATES
```
public static final String SCRIPT_DELAY_FOR_FILE_UPDATES
```
    Config List property: "script.fileRefreshDelay"
    In some cases, especially with virtualization, there may be delays between before the program is able to register file system changes made by another container/node/host. After module scripts have completed, wait this many seconds before taking any action. This allows the file system to reflect all changes.
    
    See Also:
    
    Constant Field Values
  - SCRIPT_DIR
```
public static final String SCRIPT_DIR
```
    Name of the script sub-directory: "script"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_FAILURES
```
public static final String SCRIPT_FAILURES
```
    File suffix appended to failed scripts: "Failures"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_NUM_THREADS
```
public static final String SCRIPT_NUM_THREADS
```
    Config Integer property: "script.numThreads"
    "Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter."
    
    See Also:
    
    Constant Field Values
  - SCRIPT_NUM_THREADS_DESC
```
public static final String SCRIPT_NUM_THREADS_DESC
```
    See Also:
    
    Constant Field Values
  - SCRIPT_NUM_WORKERS
```
public static final String SCRIPT_NUM_WORKERS
```
    Config Integer property: "script.numWorkers"
    "Set number of samples to process per script (if parallel processing)"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_NUM_WORKERS_DESC
```
public static final String SCRIPT_NUM_WORKERS_DESC
```
    See Also:
    
    Constant Field Values
  - SCRIPT_PERMISSIONS
```
public static final String SCRIPT_PERMISSIONS
```
    Config String property: "script.permissions"
    "Used as chmod permission parameter (ex: 774)"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_PERMISSIONS_DESC
```
public static final String SCRIPT_PERMISSIONS_DESC
```
    See Also:
    
    Constant Field Values
  - SCRIPT_STARTED
```
public static final String SCRIPT_STARTED
```
    File suffix appended to started script: "Started"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_SUCCESS
```
public static final String SCRIPT_SUCCESS
```
    File suffix appended to successful scripts: "Success"
    
    See Also:
    
    Constant Field Values
  - SCRIPT_TIMEOUT
```
public static final String SCRIPT_TIMEOUT
```
    Config Integer property: "script.timeout"
    "Sets # of minutes before worker scripts times out."
    
    See Also:
    
    Constant Field Values
  - SCRIPT_TIMEOUT_DESC
```
public static final String SCRIPT_TIMEOUT_DESC
```
    See Also:
    
    Constant Field Values
  - SET_SEED
```
public static final String SET_SEED
```
    Config property "pipeline.setSeed"
    
    See Also:
    
    Constant Field Values
  - SH_EXT
```
public static final String SH_EXT
```
    BioLockJ shell script file extension: ".sh"
    
    See Also:
    
    Constant Field Values
  - SPECIES
```
public static final String SPECIES
```
    Config option for "report.taxonomyLevels": "species"
    
    See Also:
    
    Constant Field Values
  - STANDARD_CONFIG_PATH
```
public static final String STANDARD_CONFIG_PATH
```
    Default Config imported for all pipelines (if file exists)
    
    See Also:
    
    Constant Field Values
  - STATUS_MARK_KEY
```
public static final String STATUS_MARK_KEY
```
    Key used in standard err messages indicating that this line should be shown to the user. This should only be used for very minimal messaging to explain long delays. Unlike #STATUS_UPDATE_KEY, this is used for overwriting updates, such as short animations, progress bars, etc. See ProgressUtil; lines with this key will be used print a line at launch replacing any current spinner. This should be used to mark the completion of a potentially lengthy process was used STATUS_START_KEY at the start.
    
    See Also:
    
    STATUS_START_KEY, Constant Field Values
  - STATUS_START_KEY
```
public static final String STATUS_START_KEY
```
    Key used in standard err messages indicating that this line should be shown to the user. This should only be used for very minimal messaging to explain long delays. See ProgressUtil; lines with this key will be used to start a spinner, and should be printed at the start of a potentially lengthy process.
    
    See Also:
    
    STATUS_MARK_KEY, Constant Field Values
  - TAB_DELIM
```
public static final String TAB_DELIM
```
    BioLockJ tab character: "\t"
    
    See Also:
    
    Constant Field Values
  - TRUE
```
public static final String TRUE
```
    Boolean Config property value option: "Y"
    
    See Also:
    
    Constant Field Values
  - TSV_EXT
```
public static final String TSV_EXT
```
    BioLockJ tab delimited text file extension: ".tsv"
    
    See Also:
    
    Constant Field Values
  - TXT_EXT
```
public static final String TXT_EXT
```
    BioLockJ standard text file extension: ".txt"
    
    See Also:
    
    Constant Field Values
  - UNCLASSIFIED
```
public static final String UNCLASSIFIED
```
    Unclassified taxa prefix: "Unclassified"
    
    See Also:
    
    Constant Field Values
  - USER_PROFILE
```
public static final String USER_PROFILE
```
    Config File property: "pipeline.userProfile"
    
    See Also:
    
    Constant Field Values
  - VERSION
```
public static final String VERSION
```
    BioLockJ main() runtime arg used to print version info: "-version"
    
    See Also:
    
    Constant Field Values
  - VALIDATION_ENABLED
```
public static final String VALIDATION_ENABLED
```
    String used by sheepdog_testing_suite to assert that validation is enabled: "This pipeline has validation enabled.".
    
    See Also:
    
    Constant Field Values
  - UNVERIFIED_PROPS_FILE
```
public static final String UNVERIFIED_PROPS_FILE
```
    See Also:
    
    Constant Field Values
  - YEAR_AND_OWNER
```
public static final String YEAR_AND_OWNER
```
    The year and owner of this program as of most recent development.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Constants
```
public Constants()
```
- Method Detail
  - registerProps
```
static final void registerProps()
                         throws API_Exception
```
    Register properties with the Properties class for API access.
    
    Throws:
    
    API_Exception

Class Constants

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

APP_START_TIME

ASSIGN_ALIAS

AWS_S3_XFER_TIMEOUT

BASH_PROFILE

BASH_RC

BLJ_COMPLETE

BLJ_FAILED

BLJ_MODULE_TAG

BLJ_STARTED

BLJ_VERSION_PROP

BLJ_VERSION_PROP_DESC

BLJ_WIKI

CLASS

CLUSTER_HOST

DEFAULT_MOD_DEMUX

DEFAULT_MOD_FASTA_CONV

DEFAULT_MOD_SEQ_MERGER

DEFAULT_STATS_MODULE

DELIM_SEP

DETACH_JAVA_MODULES

DEVELOPER_NOTE

DISABLE_ADD_IMPLICIT_MODULES

DISABLE_PRE_REQ_MODULES

DOCKER_CONFIG_PATH

DOCKER_EXE_PREFIX

DOMAIN

DOWNLOAD_DIR

EXE_PREFIX

EXE_AWK

EXE_DOCKER

EXE_GZIP

EXE_JAVA

EXE_PYTHON

EXE_RSCRIPT

FALSE

FAMILY

FASTA

FASTQ

GENUS

GZIP_EXT

HELP

HOST_EXE_PREFIX

HN2_DISABLE_GENE_FAMILIES

HN2_DISABLE_PATH_ABUNDANCE

HN2_DISABLE_PATH_COVERAGE

HN2_GENE_FAM_SUM

HN2_PATH_ABUND_SUM

HN2_PATH_COVG_SUM

HN2_TOTAL_PATH_COUNT

HN2_UNIQUE_PATH_COUNT

INDENT

INPUT_ALLOW_DUPS

INPUT_DIRS

INPUT_FORWARD_READ_SUFFIX

INPUT_IGNORE_FILES

INPUT_REQUIRE_COMPLETE_PAIRS

INPUT_REQUIRE_COMPLETE_PAIRS_DESC

INPUT_REVERSE_READ_SUFFIX

INPUT_TRIM_PREFIX

INPUT_TRIM_SUFFIX

INPUT_TYPES

INTERNAL_PREFIX

INTERNAL_ALL_MODULES

INTERNAL_BLJ_MODULE

INTERNAL_DEFAULT_CONFIG

INTERNAL_IS_MULTI_LINE_SEQ

INTERNAL_MULTIPLEXED

INTERNAL_PAIRED_READS

INTERNAL_PIPELINE_DIR

INTERNAL_PIPELINE_NAME

INTERNAL_PIPELINE_ID

INTERNAL_SEQ_HEADER_CHAR

INTERNAL_SEQ_TYPE

JAR_ARG