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`	`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_WIKI` URL to the BioLockJ WIKI
`static String`	`CLASS` `Config` option for "report.taxonomyLevels": "class"
`static String`	`DEFAULT_MOD_DEMUX` `Config` String property: Java class name for default module used to demultiplex data: "pipeline.defaultDemultiplexer"
`static String`	`DEFAULT_MOD_FASTA_CONV` `Config` String property: Java class name for default module used to convert files into fasta: "pipeline.defaultFastaConverter" format
`static String`	`DEFAULT_MOD_SEQ_MERGER` `Config` String property: Java class name for default module used combined paired read files: "pipeline.defaultSeqMerger"
`static String`	`DEFAULT_STATS_MODULE` `Config` String property: Java class name for default module used generate p-value and other stats: "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` Boolean property: "pipeline.detachJavaModules" If "Y" Java modules do not run with main BioLockJ Java application
`static String`	`DISABLE_ADD_IMPLICIT_MODULES` `Config` Boolean property: "pipeline.disableAddImplicitModules" If set to "Y", implicit modules will not be added to the pipeline.
`static String`	`DISABLE_PRE_REQ_MODULES` `Config` Boolean property: "pipeline.disableAddPreReqModules" If set to "Y", prerequisite modules will not be added to the pipeline.
`static String`	`DOCKER_CONFIG_PATH` Default Docker `Config` file imported after "${BLJ}/resources/config/default/standard.properties" (if files exist)
`static String`	`DOMAIN` `Config` option for "report.taxonomyLevels": "domain"
`static String`	`EXE_AWK` `Config` String property: "exe.awk" Set command line executable awk.
`static String`	`EXE_DOCKER` `Config` String property "exe.docker" Set command line executable docker
`static String`	`EXE_GZIP` `Config` String property "exe.gzip" Set command line executable gzip
`static String`	`EXE_JAVA` `Config` property for java executable: "exe.java"
`static String`	`EXE_PYTHON` `Config` property to python executable
`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 constant: ".gz"
`static String`	`HN2_DISABLE_GENE_FAMILIES` `Config` Boolean property to disable HumanN2 Gene Family report: "humann2.disableGeneFamilies"
`static String`	`HN2_DISABLE_PATH_ABUNDANCE` `Config` Boolean property to disable HumanN2 Pathway Abundance report: "humann2.disablePathAbundance"
`static String`	`HN2_DISABLE_PATH_COVERAGE` `Config` Boolean property to disable HumanN2 Pathway Coverage report: "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`	`INDENT` Standard indent = 4 spaces.
`static String`	`INPUT_DIRS` `Config` List property: "input.dirPaths" Set sequence file directories
`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" Set file names to ignore if found in "input.dirPaths"
`static String`	`INPUT_REQUIRE_COMPLETE_PAIRS` `Config` Boolean property: "input.requireCompletePairs" Require 100% sequence input files are matching paired reads
`static String`	`INPUT_REVERSE_READ_SUFFIX` `Config` String property: "input.suffixRv" Set file suffix used to identify forward reads in "input.dirPaths"
`static String`	`INPUT_TRIM_PREFIX` `Config` String property: "input.trimPrefix" Set value of prefix to trim from sequence file names or headers to obtain Sample ID.
`static String`	`INPUT_TRIM_SEQ_FILE` `Config` property "trimPrimers.filePath" defines the file path to the file that defines the primers as regular expressions.
`static String`	`INPUT_TRIM_SUFFIX` `Config` String property: "input.trimSuffix" Set value of suffix to trim from sequence file names or headers to obtain Sample ID.
`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_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`	`LIMIT_DEBUG_CLASSES` `Config` property used to limit classes that log debug statements when "pipeline.logLevel"="Y"
`static String`	`LOG_EXT` BioLockJ log file extension constant: ".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`	`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_TABLE_PREFIX` QIIME OTU table prefix: "otu_table"
`static String`	`PARAMS` `Config` property suffix for exe.* properties, used to set optional parameters: "Params"
`static String`	`PDF_EXT` BioLockJ PDF file extension constant: ".pdf"
`static String`	`PHYLUM` `Config` option for "report.taxonomyLevels": "phylum"
`static String`	`PIPELINE_COPY_FILES` `Config` property set to copy input files into pipeline root directory: "pipeline.copyInput"
`static String`	`PIPELINE_DEFAULT_PROPS` `Config` String property: "pipeline.defaultProps" Set file path of default property file.
`static String`	`PIPELINE_DELETE_TEMP_FILES` `Config` property set to delete `BioModule.getTempDir()` files: "pipeline.deleteTempFiles"
`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` Boolean property: "pipeline.env" Options: "cluster", "aws", "local"
`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_NAME` `Config` property to assign a name to a pipeline: "pipeline.name" TODO: needs to be implemented.
`static String`	`PROCESSED` File suffix appended to processed samples in the module output directory: "_reported.tsv"
`static String`	`PROJECT_DESC` `Config` property to assign a free-hand to a project: "project.desc" 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.
`protected static String`	`PROJECT_PERMISSIONS` `Config` property to define permission settings when running chmod on pipeline root dir: "pipeline.permissions"
`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_EXT` File extension of BioLockJ generated R Scripts: ".R"
`static String`	`R_INTERNAL_RUN_HN2` `Config` Boolean property to signal R scripts to build HumanN2 reports
`static String`	`R_PLOT_EFFECT_SIZE_DISABLE_FC` `Config` Boolean property to disable fold change plots: "r_PlotEffectSize.disableFoldChange"
`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`	`RETURN` Return character constant backslash-n
`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_STARTED` File suffix appended to started script: "Started"
`static String`	`SCRIPT_SUCCESS` File suffix appended to successful scripts: "Success"
`static String`	`SEPARATOR` Semi-colon is used to separate each taxa "\|"
`static String`	`SH_EXT` BioLockJ shell script file extension constant: ".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`	`TAB_DELIM` BioLockJ tab character constant: "\t"
`static String`	`TRUE` Boolean `Config` property value option: "Y"
`static String`	`TSV_EXT` BioLockJ tab delimited text file extension constant: ".tsv"
`static String`	`TXT_EXT` BioLockJ standard text file extension constant: ".txt"

Constructor Summary

Constructors
Constructor and Description

Constants()

Constructors
Constructor and Description
`Constants()`

Method Summary
- 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
  - 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_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
  - DEFAULT_MOD_DEMUX
```
public static final String DEFAULT_MOD_DEMUX
```
    Config String property: Java class name for default module used to demultiplex data: "pipeline.defaultDemultiplexer"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MOD_FASTA_CONV
```
public static final String DEFAULT_MOD_FASTA_CONV
```
    Config String property: Java class name for default module used to convert files into fasta: "pipeline.defaultFastaConverter" format
    
    See Also:
    
    Constant Field Values
  - DEFAULT_MOD_SEQ_MERGER
```
public static final String DEFAULT_MOD_SEQ_MERGER
```
    Config String property: Java class name for default module used combined paired read files: "pipeline.defaultSeqMerger"
    
    See Also:
    
    Constant Field Values
  - DEFAULT_STATS_MODULE
```
public static final String DEFAULT_STATS_MODULE
```
    Config String property: Java class name for default module used generate p-value and other stats: "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 Boolean property: "pipeline.detachJavaModules"
    If "Y" Java modules do not run with main BioLockJ Java application
    
    See Also:
    
    Constant Field Values
  - DISABLE_ADD_IMPLICIT_MODULES
```
public static final String DISABLE_ADD_IMPLICIT_MODULES
```
    Config Boolean property: "pipeline.disableAddImplicitModules"
    If set to "Y", implicit modules will not be added to the pipeline.
    
    See Also:
    
    Constant Field Values
  - DISABLE_PRE_REQ_MODULES
```
public static final String DISABLE_PRE_REQ_MODULES
```
    Config Boolean property: "pipeline.disableAddPreReqModules"
    If set to "Y", prerequisite modules will not be added to the pipeline.
    
    See Also:
    
    Constant Field Values
  - DOCKER_CONFIG_PATH
```
public static final String DOCKER_CONFIG_PATH
```
    Default Docker Config file imported after "${BLJ}/resources/config/default/standard.properties" (if files exist)
    
    See Also:
    
    Constant Field Values
  - DOMAIN
```
public static final String DOMAIN
```
    Config option for "report.taxonomyLevels": "domain"
    
    See Also:
    
    Constant Field Values
  - EXE_AWK
```
public static final String EXE_AWK
```
    Config String property: "exe.awk"
    Set command line executable awk.
    
    See Also:
    
    Constant Field Values
  - EXE_DOCKER
```
public static final String EXE_DOCKER
```
    Config String property "exe.docker"
    Set command line executable docker
    
    See Also:
    
    Constant Field Values
  - EXE_GZIP
```
public static final String EXE_GZIP
```
    Config String property "exe.gzip"
    Set command line executable gzip
    
    See Also:
    
    Constant Field Values
  - EXE_JAVA
```
public static final String EXE_JAVA
```
    Config property for java executable: "exe.java"
    
    See Also:
    
    Constant Field Values
  - EXE_PYTHON
```
public static final String EXE_PYTHON
```
    Config property to python executable
    
    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 constant: ".gz"
    
    See Also:
    
    Constant Field Values
  - HN2_DISABLE_GENE_FAMILIES
```
public static final String HN2_DISABLE_GENE_FAMILIES
```
    Config Boolean property to disable HumanN2 Gene Family report: "humann2.disableGeneFamilies"
    
    See Also:
    
    Constant Field Values
  - HN2_DISABLE_PATH_ABUNDANCE
```
public static final String HN2_DISABLE_PATH_ABUNDANCE
```
    Config Boolean property to disable HumanN2 Pathway Abundance report: "humann2.disablePathAbundance"
    
    See Also:
    
    Constant Field Values
  - HN2_DISABLE_PATH_COVERAGE
```
public static final String HN2_DISABLE_PATH_COVERAGE
```
    Config Boolean property to disable HumanN2 Pathway Coverage report: "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_DIRS
```
public static final String INPUT_DIRS
```
    Config List property: "input.dirPaths"
    Set sequence file directories
    
    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"
    Set file names to ignore if found in "input.dirPaths"
    
    See Also:
    
    Constant Field Values
  - INPUT_REQUIRE_COMPLETE_PAIRS
```
public static final String INPUT_REQUIRE_COMPLETE_PAIRS
```
    Config Boolean property: "input.requireCompletePairs"
    Require 100% sequence input files are matching paired reads
    
    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 forward reads in "input.dirPaths"
    
    See Also:
    
    Constant Field Values
  - INPUT_TRIM_PREFIX
```
public static final String INPUT_TRIM_PREFIX
```
    Config String property: "input.trimPrefix"
    Set value of prefix to trim from sequence file names or headers to obtain Sample ID.
    
    See Also:
    
    Constant Field Values
  - INPUT_TRIM_SEQ_FILE
```
public static final String INPUT_TRIM_SEQ_FILE
```
    Config property "trimPrimers.filePath" defines the file path to the file that defines the primers as regular expressions.
    
    See Also:
    
    Constant Field Values
  - INPUT_TRIM_SUFFIX
```
public static final String INPUT_TRIM_SUFFIX
```
    Config String property: "input.trimSuffix"
    Set value of suffix to trim from sequence file names or headers to obtain Sample ID.
    
    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_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
  - LIMIT_DEBUG_CLASSES
```
public static final String LIMIT_DEBUG_CLASSES
```
    Config property used to limit classes that log debug statements when "pipeline.logLevel"="Y"
    
    See Also:
    
    Constant Field Values
  - LOG_EXT
```
public static final String LOG_EXT
```
    BioLockJ log file extension constant: ".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
  - 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_TABLE_PREFIX
```
public static final String OTU_TABLE_PREFIX
```
    QIIME OTU table prefix: "otu_table"
    
    See Also:
    
    Constant Field Values
  - PARAMS
```
public static final String PARAMS
```
    Config property suffix for exe.* properties, used to set optional parameters: "Params"
    
    See Also:
    
    Constant Field Values
  - PDF_EXT
```
public static final String PDF_EXT
```
    BioLockJ PDF file extension constant: ".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 set to copy input files into pipeline root directory: "pipeline.copyInput"
    
    See Also:
    
    Constant Field Values
  - PIPELINE_DEFAULT_PROPS
```
public static final String PIPELINE_DEFAULT_PROPS
```
    Config String property: "pipeline.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
  - PIPELINE_DELETE_TEMP_FILES
```
public static final String PIPELINE_DELETE_TEMP_FILES
```
    Config property set to delete BioModule.getTempDir() files: "pipeline.deleteTempFiles"
    
    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 Boolean property: "pipeline.env"
    Options: "cluster", "aws", "local"
    
    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_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
  - 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_DESC
```
public static final String PROJECT_DESC
```
    Config property to assign a free-hand to a project: "project.desc" 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
  - 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
  - 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
  - R_PLOT_EFFECT_SIZE_DISABLE_FC
```
public static final String R_PLOT_EFFECT_SIZE_DISABLE_FC
```
    Config Boolean property to disable fold change plots: "r_PlotEffectSize.disableFoldChange"
    
    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
  - RETURN
```
public static final String RETURN
```
    Return character constant *backslash-n*
    
    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_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
  - SEPARATOR
```
public static final String SEPARATOR
```
    Semi-colon is used to separate each taxa "|"
    
    See Also:
    
    Constant Field Values
  - SH_EXT
```
public static final String SH_EXT
```
    BioLockJ shell script file extension constant: ".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
  - TAB_DELIM
```
public static final String TAB_DELIM
```
    BioLockJ tab character constant: "\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 constant: ".tsv"
    
    See Also:
    
    Constant Field Values
  - TXT_EXT
```
public static final String TXT_EXT
```
    BioLockJ standard text file extension constant: ".txt"
    
    See Also:
    
    Constant Field Values
  - PROJECT_PERMISSIONS
```
protected static final String PROJECT_PERMISSIONS
```
    Config property to define permission settings when running chmod on pipeline root dir: "pipeline.permissions"
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Constants
```
public Constants()
```

Class Constants

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

APP_START_TIME

BLJ_COMPLETE

BLJ_FAILED

BLJ_MODULE_TAG

BLJ_STARTED

BLJ_WIKI

CLASS

DEFAULT_MOD_DEMUX

DEFAULT_MOD_FASTA_CONV

DEFAULT_MOD_SEQ_MERGER

DEFAULT_STATS_MODULE

DELIM_SEP

DETACH_JAVA_MODULES

DISABLE_ADD_IMPLICIT_MODULES

DISABLE_PRE_REQ_MODULES

DOCKER_CONFIG_PATH

DOMAIN

EXE_AWK

EXE_DOCKER

EXE_GZIP

EXE_JAVA

EXE_PYTHON

FALSE

FAMILY

FASTA

FASTQ

GENUS

GZIP_EXT

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_DIRS

INPUT_FORWARD_READ_SUFFIX

INPUT_IGNORE_FILES

INPUT_REQUIRE_COMPLETE_PAIRS

INPUT_REVERSE_READ_SUFFIX

INPUT_TRIM_PREFIX

INPUT_TRIM_SEQ_FILE

INPUT_TRIM_SUFFIX

INTERNAL_ALL_MODULES

INTERNAL_BLJ_MODULE

INTERNAL_DEFAULT_CONFIG

INTERNAL_IS_MULTI_LINE_SEQ

INTERNAL_MULTIPLEXED

INTERNAL_PAIRED_READS

INTERNAL_PIPELINE_DIR

INTERNAL_SEQ_HEADER_CHAR

INTERNAL_SEQ_TYPE

LIMIT_DEBUG_CLASSES

LOG_EXT

LOG_LEVEL_PROPERTY

LOG_SPACER

MASTER_PREFIX

MODULE_SEQ_PACKAGE

MODULE_WGS_CLASSIFIER_PACKAGE

ORDER

OTU_COUNT

OTU_TABLE_PREFIX

PARAMS

PDF_EXT

PHYLUM

PIPELINE_COPY_FILES

PIPELINE_DEFAULT_PROPS

PIPELINE_DELETE_TEMP_FILES

PIPELINE_DESC

PIPELINE_ENV

PIPELINE_ENV_AWS

PIPELINE_ENV_CLUSTER