Constant Field Values

Contents

• biolockj.*

biolockj.*

biolockj.Constants

Modifier and Type	Constant Field	Value
public static final String	BLJ_COMPLETE	"biolockjComplete"
public static final String	BLJ_FAILED	"biolockjFailed"
public static final String	BLJ_MODULE_TAG	"#BioModule"
public static final String	BLJ_STARTED	"biolockjStarted"
public static final String	BLJ_WIKI	"https://github.com/msioda/BioLockJ/wiki"
public static final String	CLASS	"class"
public static final String	DEFAULT_MOD_DEMUX	"pipeline.defaultDemultiplexer"
public static final String	DEFAULT_MOD_FASTA_CONV	"pipeline.defaultFastaConverter"
public static final String	DEFAULT_MOD_SEQ_MERGER	"pipeline.defaultSeqMerger"
public static final String	DEFAULT_STATS_MODULE	"pipeline.defaultStatsModule"
public static final String	DELIM_SEP	"__"
public static final String	DETACH_JAVA_MODULES	"pipeline.detachJavaModules"
public static final String	DISABLE_ADD_IMPLICIT_MODULES	"pipeline.disableAddImplicitModules"
public static final String	DISABLE_PRE_REQ_MODULES	"pipeline.disableAddPreReqModules"
public static final String	DOCKER_CONFIG_PATH	"${BLJ}/resources/config/default/docker.properties"
public static final String	DOMAIN	"domain"
public static final String	EXE_AWK	"exe.awk"
public static final String	EXE_DOCKER	"exe.docker"
public static final String	EXE_GZIP	"exe.gzip"
public static final String	EXE_JAVA	"exe.java"
public static final String	EXE_PYTHON	"exe.python"
public static final String	FALSE	"N"
public static final String	FAMILY	"family"
public static final String	FASTA	"fasta"
public static final String	FASTQ	"fastq"
public static final String	GENUS	"genus"
public static final String	GZIP_EXT	".gz"
public static final String	HN2_DISABLE_GENE_FAMILIES	"humann2.disableGeneFamilies"
public static final String	HN2_DISABLE_PATH_ABUNDANCE	"humann2.disablePathAbundance"
public static final String	HN2_DISABLE_PATH_COVERAGE	"humann2.disablePathCoverage"
public static final String	HN2_GENE_FAM_SUM	"geneFam"
public static final String	HN2_PATH_ABUND_SUM	"pAbund"
public static final String	HN2_PATH_COVG_SUM	"pCovg"
public static final String	HN2_TOTAL_PATH_COUNT	"Total_Pathways"
public static final String	HN2_UNIQUE_PATH_COUNT	"Unique_Pathways"
public static final String	INDENT	" "
public static final String	INPUT_DIRS	"input.dirPaths"
public static final String	INPUT_FORWARD_READ_SUFFIX	"input.suffixFw"
public static final String	INPUT_IGNORE_FILES	"input.ignoreFiles"
public static final String	INPUT_REQUIRE_COMPLETE_PAIRS	"input.requireCompletePairs"
public static final String	INPUT_REVERSE_READ_SUFFIX	"input.suffixRv"
public static final String	INPUT_TRIM_PREFIX	"input.trimPrefix"
public static final String	INPUT_TRIM_SEQ_FILE	"trimPrimers.filePath"
public static final String	INPUT_TRIM_SUFFIX	"input.trimSuffix"
public static final String	INTERNAL_ALL_MODULES	"internal.allModules"
public static final String	INTERNAL_BLJ_MODULE	"internal.configModules"
public static final String	INTERNAL_DEFAULT_CONFIG	"internal.defaultConfig"
public static final String	INTERNAL_IS_MULTI_LINE_SEQ	"internal.isMultiLineSeq"
public static final String	INTERNAL_MULTIPLEXED	"internal.multiplexed"
public static final String	INTERNAL_PAIRED_READS	"internal.pairedReads"
public static final String	INTERNAL_PIPELINE_DIR	"internal.pipelineDir"
public static final String	INTERNAL_SEQ_HEADER_CHAR	"internal.seqHeaderChar"
public static final String	INTERNAL_SEQ_TYPE	"internal.seqType"
public static final String	LIMIT_DEBUG_CLASSES	"pipeline.limitDebugClasses"
public static final String	LOG_EXT	".log"
public static final String	LOG_LEVEL_PROPERTY	"pipeline.logLevel"
public static final String	LOG_SPACER	"========================================================================"
public static final String	MASTER_PREFIX	"MASTER_"
public static final String	MODULE_SEQ_PACKAGE	"biolockj.module.seq"
public static final String	MODULE_WGS_CLASSIFIER_PACKAGE	"biolockj.module.classifier.wgs"
public static final String	ORDER	"order"
public static final String	OTU_COUNT	"otuCount"
public static final String	OTU_TABLE_PREFIX	"otu_table"
public static final String	PARAMS	"Params"
public static final String	PDF_EXT	".pdf"
public static final String	PHYLUM	"phylum"
public static final String	PIPELINE_COPY_FILES	"pipeline.copyInput"
public static final String	PIPELINE_DEFAULT_PROPS	"pipeline.defaultProps"
public static final String	PIPELINE_DELETE_TEMP_FILES	"pipeline.deleteTempFiles"
public static final String	PIPELINE_DESC	"pipeline.desc"
public static final String	PIPELINE_ENV	"pipeline.env"
public static final String	PIPELINE_ENV_AWS	"aws"
public static final String	PIPELINE_ENV_CLUSTER	"cluster"
public static final String	PIPELINE_ENV_LOCAL	"local"
public static final String	PIPELINE_NAME	"pipeline.name"
public static final String	PROCESSED	"_reported.tsv"
public static final String	PROJECT_DESC	"project.desc"
public static final String	PROJECT_NAME	"project.name"
protected static final String	PROJECT_PERMISSIONS	"pipeline.permissions"
public static final String	QIIME	"qiime"
public static final String	QIIME_ALPHA_DIVERSITY_METRICS	"qiime.alphaMetrics"
public static final String	QIIME_BARCODE_SEQ_COL	"BarcodeSequence"
public static final String	QIIME_DEMUX_COL	"BioLockJFileName"
public static final String	QIIME_DESC_COL	"Description"
public static final String	QIIME_LINKER_PRIMER_SEQ_COL	"LinkerPrimerSequence"
public static final String	R_EXT	".R"
public static final String	R_INTERNAL_RUN_HN2	"R_internal.runHumann2"
public static final String	R_PLOT_EFFECT_SIZE_DISABLE_FC	"r_PlotEffectSize.disableFoldChange"
public static final String	RDP_THRESHOLD_SCORE	"rdp.minThresholdScore"
public static final String	REPORT_LOG_BASE	"report.logBase"
public static final String	REPORT_MIN_COUNT	"report.minCount"
public static final String	REPORT_NUM_HITS	"report.numHits"
public static final String	REPORT_NUM_READS	"report.numReads"
public static final String	REPORT_SAMPLE_CUTOFF	"report.scarceSampleCutoff"
public static final String	REPORT_SCARCE_CUTOFF	"report.scarceCountCutoff"
public static final String	REPORT_TAXONOMY_LEVELS	"report.taxonomyLevels"
public static final String	RETURN	"\n"
public static final String	SCRIPT_DIR	"script"
public static final String	SCRIPT_FAILURES	"Failures"
public static final String	SCRIPT_STARTED	"Started"
public static final String	SCRIPT_SUCCESS	"Success"
public static final String	SEPARATOR	"|"
public static final String	SH_EXT	".sh"
public static final String	SPECIES	"species"
public static final String	STANDARD_CONFIG_PATH	"${BLJ}/resources/config/default/standard.properties"
public static final String	TAB_DELIM	"\t"
public static final String	TRUE	"Y"
public static final String	TSV_EXT	".tsv"
public static final String	TXT_EXT	".txt"

biolockj.Log

Modifier and Type	Constant Field	Value
protected static final String	DEFAULT_FORMAT	"%d{yyyy-MM-dd HH:mm:ss} %p %c{1}: %m%n"
protected static final String	DIRECT_FORMAT	"%m%n"
protected static final String	LOG_APPEND	"LOG_APPEND"
protected static final String	LOG_FILE	"LOG_FILE"

biolockj.exception.*

biolockj.exception.ConfigPathException

Modifier and Type	Constant Field	Value
public static final String	DIRECTORY	"directory"
public static final String	FILE	"file"

biolockj.module.*

biolockj.module.BioModule

Modifier and Type	Constant Field	Value
public static final String	MAIN_SCRIPT_PREFIX	"MAIN_"
public static final String	OUTPUT_DIR	"output"
public static final String	TEMP_DIR	"temp"

biolockj.module.BioModuleImpl

Modifier and Type	Constant Field	Value
public static final String	GZIP_EXT	".gz"
public static final String	LOG_EXT	".log"
public static final String	PDF_EXT	".pdf"
public static final String	RETURN	"\n"
public static final String	SH_EXT	".sh"
public static final String	TAB_DELIM	"\t"
public static final String	TSV_EXT	".tsv"
public static final String	TXT_EXT	".txt"

biolockj.module.JavaModuleImpl

Modifier and Type	Constant Field	Value
protected static final String	BLJ_OPTIONS	"BLJ_OPTIONS"

biolockj.module.ScriptModule

Modifier and Type	Constant Field	Value
public static final String	SCRIPT_BATCH_SIZE	"script.batchSize"
public static final String	SCRIPT_DEFAULT_HEADER	"script.defaultHeader"
public static final String	SCRIPT_NUM_THREADS	"script.numThreads"
public static final String	SCRIPT_PERMISSIONS	"script.permissions"
public static final String	SCRIPT_TIMEOUT	"script.timeout"

biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Modifier and Type	Constant Field	Value
protected static final String	BATCH_MAPPING	"batchMapping.tsv"
protected static final String	FUNCTION_CREATE_BATCH_MAPPING	"createBatchMapping"
public static final String	PICK_OTU_SCRIPT	"pick_closed_reference_otus.py"

biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Modifier and Type	Constant Field	Value
public static final String	PICK_OTU_SCRIPT	"pick_de_novo_otus.py"

biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Modifier and Type	Constant Field	Value
public static final String	PICK_OTU_SCRIPT	"pick_open_reference_otus.py"

biolockj.module.classifier.r16s.RdpClassifier

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_RDP	"runRdp"
protected static final String	RDP_DB	"rdp.db"
protected static final String	RDP_JAR	"rdp.jar"
protected static final String	RDP_PARAMS	"exe.rdpParams"

biolockj.module.classifier.wgs.Humann2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_HUMANN2	"exe.humann2"
protected static final String	EXE_HUMANN2_JOIN_PARAMS	"exe.humann2JoinTableParams"
protected static final String	EXE_HUMANN2_PARAMS	"exe.humann2Params"
protected static final String	EXE_HUMANN2_RENORM_PARAMS	"exe.humann2RenormTableParams"
protected static final String	HN2_NUCL_DB	"humann2.nuclDB"
protected static final String	HN2_PROT_DB	"humann2.protDB"

biolockj.module.classifier.wgs.Kraken2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_KRAKEN2	"exe.kraken2"
protected static final String	FUNCTION_KRAKEN	"runKraken2"
protected static final String	KRAKEN_DATABASE	"kraken2.db"
protected static final String	KRAKEN_FILE	"_kraken2_out.txt"

biolockj.module.classifier.wgs.KrakenClassifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_KRAKEN	"exe.kraken"
protected static final String	FUNCTION_KRAKEN	"runKraken"
protected static final String	FUNCTION_TRANSLATE	"translate"
protected static final String	KRAKEN_DATABASE	"kraken.db"
protected static final String	KRAKEN_FILE	"_kraken_out.txt"

biolockj.module.classifier.wgs.Metaphlan2Classifier

Modifier and Type	Constant Field	Value
protected static final String	EXE_METAPHLAN	"exe.metaphlan2"
protected static final String	EXE_METAPHLAN_PARAMS	"exe.metaphlan2Params"
protected static final String	METAPHLAN2_DB	"metaphlan2.db"
protected static final String	METAPHLAN2_MPA_PKL	"metaphlan2.mpa_pkl"

biolockj.module.implicit.Demultiplexer

Modifier and Type	Constant Field	Value
protected static final int	NUM_LINES_TEMP_FILE	2000000
protected static final String	SAMPLE_ID_SUFFIX_TRIM_DEFAULT	"_"

biolockj.module.implicit.RegisterNumReads

Modifier and Type	Constant Field	Value
protected static final String	NUM_READS	"Num_Reads"

biolockj.module.implicit.parser.ParserModuleImpl

Modifier and Type	Constant Field	Value
protected static final String	NUM_OTUS	"OTU_COUNT"

biolockj.module.implicit.parser.wgs.Humann2Parser

Modifier and Type	Constant Field	Value
protected static final String	HN2_KEEP_UNINTEGRATED	"humann2.keepUnintegrated"
protected static final String	HN2_KEEP_UNMAPPED	"humann2.keepUnmapped"

biolockj.module.implicit.qiime.BuildQiimeMapping

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_REORDER_FIELDS	"reorderColumns"
protected static final String	QIIME_COMMENT	"BioLockJ Generated Mapping"
protected static final String	QIIME_ID	"#SampleID"
protected static final String	SCRIPT_VALIDATE_MAPPING	"validate_mapping_file.py"
protected static final String	VALIDATED_MAPPING	"_corrected.txt"

biolockj.module.implicit.qiime.MergeQiimeOtuTables

Modifier and Type	Constant Field	Value
protected static final String	SCRIPT_MERGE_OTU_TABLES	"merge_otu_tables.py"

biolockj.module.implicit.qiime.QiimeClassifier

Modifier and Type	Constant Field	Value
protected static final String	ALPHA_DIV_NULL_VALUE	"N/A"
protected static final String	ALPHA_DIVERSITY_TABLE	"alphaDiversity.txt"
protected static final String	COMBINED_FNA	"combined_seqs.fna"
protected static final String	EXE_VSEARCH	"exe.vsearch"
protected static final String	EXE_VSEARCH_PARAMS	"exe.vsearchParams"
protected static final String	OTU_SUMMARY_FILE	"otuSummary.txt"
protected static final String	OTU_TABLE	"otu_table.biom"
protected static final String	QIIME_PARAMS	"qiime.params"
protected static final String	QIIME_PYNAST_ALIGN_DB	"qiime.pynastAlignDB"
protected static final String	QIIME_REF_SEQ_DB	"qiime.refSeqDB"
protected static final String	QIIME_REMOVE_CHIMERAS	"qiime.removeChimeras"
protected static final String	QIIME_TAXA_DB	"qiime.taxaDB"
protected static final String	REP_SET	"rep_set"
protected static final String	SCRIPT_ADD_ALPHA_DIVERSITY	"add_alpha_to_mapping_file.py"
protected static final String	SCRIPT_ADD_LABELS	"add_qiime_labels.py"
protected static final String	SCRIPT_CALC_ALPHA_DIVERSITY	"alpha_diversity.py"
protected static final String	SCRIPT_FILTER_OTUS	"filter_otus_from_otu_table.py"
protected static final String	SCRIPT_PRINT_CONFIG	"print_qiime_config.py"
protected static final String	SCRIPT_SUMMARIZE_BIOM	"biom summarize-table"
protected static final String	SCRIPT_SUMMARIZE_TAXA	"summarize_taxa.py"
protected static final String	SUMMARIZE_TAXA_SUPPRESS_BIOM	"suppress_biom_table_output"

biolockj.module.report.Email

Modifier and Type	Constant Field	Value
public static final String	CLUSTER_HOST	"cluster.host"
protected static final String	EMAIL_ENCRYPTED_PASSWORD	"mail.encryptedPassword"
protected static final String	EMAIL_FROM	"mail.from"
protected static final String	EMAIL_HOST	"mail.smtp.host"
protected static final String	EMAIL_PORT	"mail.smtp.port"
protected static final String	EMAIL_SMTP_AUTH	"mail.smtp.auth"
protected static final String	EMAIL_START_TLS_ENABLE	"mail.smtp.starttls.enable"
protected static final String	EMAIL_TO	"mail.to"

biolockj.module.report.otu.CompileOtuCounts

Modifier and Type	Constant Field	Value
public static final String	SUMMARY	"summary"

biolockj.module.report.otu.RarefyOtuCounts

Modifier and Type	Constant Field	Value
protected static final String	LOW_ABUNDANT_CUTOFF	"rarefyOtuCounts.lowAbundantCutoff"
protected static final String	NUM_ITERATIONS	"rarefyOtuCounts.iterations"
protected static final String	QUANTILE	"rarefyOtuCounts.quantile"
protected static final String	REMOVE_LOW_ABUNDANT_SAMPLES	"rarefyOtuCounts.rmLowSamples"

biolockj.module.report.r.R_CalculateStats

Modifier and Type	Constant Field	Value
protected static final String	ADJ_PVAL_ATTRIBUTE	"ATTRIBUTE"
protected static final String	ADJ_PVAL_GLOBAL	"GLOBAL"
protected static final String	ADJ_PVAL_LOCAL	"LOCAL"
protected static final String	ADJ_PVAL_TAXA	"TAXA"
protected static final String	P_VALS_NP	"nonParametricPvals"
protected static final String	P_VALS_NP_ADJ	"adjNonParPvals"
protected static final String	P_VALS_PAR	"parametricPvals"
protected static final String	P_VALS_PAR_ADJ	"adjParPvals"
protected static final String	R_ADJ_PVALS_SCOPE	"r_CalculateStats.pAdjustScope"
protected static final String	R_PVAL_ADJ_METHOD	"r_CalculateStats.pAdjustMethod"
protected static final String	R_SQUARED_VALS	"rSquaredVals"

biolockj.module.report.r.R_Module

Modifier and Type	Constant Field	Value
public static final String	EXE_RSCRIPT	"exe.Rscript"
protected static final String	P_VAL_CUTOFF	"r.pvalCutoff"
protected static final String	R_COLOR_BASE	"r.colorBase"
protected static final String	R_COLOR_HIGHLIGHT	"r.colorHighlight"
protected static final String	R_COLOR_PALETTE	"r.colorPalette"
protected static final String	R_COLOR_POINT	"r.colorPoint"
protected static final String	R_DEBUG	"r.debug"
protected static final String	R_FUNCTION_LIB	"BioLockJ_Lib.R"
protected static final String	R_MAIN_SCRIPT	"BioLockJ_MAIN.R"
protected static final String	R_PCH	"r.pch"
protected static final String	R_RARE_OTU_THRESHOLD	"r.rareOtuThreshold"
protected static final String	R_SAVE_R_DATA	"r.saveRData"
protected static final String	R_TIMEOUT	"r.timeout"

biolockj.module.report.r.R_PlotMds

Modifier and Type	Constant Field	Value
protected static final String	R_MDS_DISTANCE	"r_PlotMds.distance"
protected static final String	R_MDS_NUM_AXIS	"r_PlotMds.numAxis"
protected static final String	R_MDS_REPORT_FIELDS	"r_PlotMds.reportFields"

biolockj.module.report.taxa.AddMetadataToTaxaTables

Modifier and Type	Constant Field	Value
public static final String	HIT_RATIO	"Hit_Ratio"
public static final String	META_MERGED	"_metaMerged.tsv"

biolockj.module.report.taxa.NormalizeTaxaTables

Modifier and Type	Constant Field	Value
protected static final String	LOG_10	"10"
protected static final String	LOG_E	"e"

biolockj.module.seq.AwkFastaConverter

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_CONVERT_454	"convert454"
protected static final String	FUNCTION_CONVERT_TO_FASTA	"convertToFastA"
protected static final String	FUNCTION_GUNZIP	"decompressGzip"

biolockj.module.seq.Gunzipper

Modifier and Type	Constant Field	Value
protected static final String	FUNCTION_GUNZIP	"openZip"

biolockj.module.seq.KneadData

Modifier and Type	Constant Field	Value
protected static final String	EXE_KNEADDATA	"exe.kneaddata"
protected static final String	EXE_KNEADDATA_PARAMS	"exe.kneaddataParams"
protected static final String	FUNCTION_SANATIZE	"sanatizeData"
protected static final String	KNEAD_DBS	"kneaddata.dbs"

biolockj.module.seq.Multiplexer

Modifier and Type	Constant Field	Value
protected static final String	DO_GZIP	"multiplexer.gzip"

biolockj.module.seq.PearMergeReads

Modifier and Type	Constant Field	Value
protected static final String	EXE_PEAR	"exe.pear"
protected static final String	EXE_PEAR_PARAMS	"exe.pearParams"
protected static final String	FUNCTION_PEAR_MERGE	"mergeReads"
public static final String	NUM_MERGED_READS	"Num_Merged_Reads"

biolockj.module.seq.RarefySeqs

Modifier and Type	Constant Field	Value
protected static final String	INPUT_RAREFYING_MAX	"rarefySeqs.max"
protected static final String	INPUT_RAREFYING_MIN	"rarefySeqs.min"
public static final String	NUM_RAREFIED_READS	"Num_Rarefied_Reads"

biolockj.module.seq.SeqFileValidator

Modifier and Type	Constant Field	Value
protected static final String	INPUT_SEQ_MAX	"seqFileValidator.seqMaxLen"
protected static final String	INPUT_SEQ_MIN	"seqFileValidator.seqMinLen"
public static final String	NUM_VALID_READS	"Num_Valid_Reads"
protected static final String	REQUIRE_EUQL_NUM_PAIRS	"seqFileValidator.requireEqualNumPairs"

biolockj.module.seq.TrimPrimers

Modifier and Type	Constant Field	Value
protected static final String	INPUT_REQUIRE_PRIMER	"trimPrimers.requirePrimer"
public static final String	NUM_TRIMMED_READS	"Num_Trimmed_Reads"

biolockj.node.*

biolockj.node.r16s.QiimeNode

Modifier and Type	Constant Field	Value
protected static final String	QIIME_DOMAIN_DELIM	"k__"
protected static final String	SILVA_CLASS_DELIM	"D_2__"
protected static final String	SILVA_DOMAIN_DELIM	"D_0__"
protected static final String	SILVA_FAMILY_DELIM	"D_4__"
protected static final String	SILVA_GENUS_DELIM	"D_5__"
protected static final String	SILVA_ORDER_DELIM	"D_3__"
protected static final String	SILVA_PHYLUM_DELIM	"D_1__"
protected static final String	SILVA_SPECIES_DELIM	"D_6__"

biolockj.util.*

biolockj.util.BashScriptBuilder

Modifier and Type	Constant Field	Value
protected static final String	CLUSTER_BATCH_COMMAND	"cluster.batchCommand"
protected static final String	CLUSTER_MODULES	"cluster.modules"
protected static final String	CLUSTER_PROLOGUE	"cluster.prologue"
protected static final String	CLUSTER_VALIDATE_PARAMS	"cluster.validateParams"
protected static final String	FUNCTION_EXECUTE	"execute"
protected static final String	FUNCTION_RUN_JOB	"runJob"
protected static final String	SCRIPT_JOB_HEADER	"cluster.jobHeader"

biolockj.util.BioLockJUtil

Modifier and Type	Constant Field	Value
public static final String	INTERNAL_PIPELINE_INPUT_TYPES	"internal.pipelineInputTypes"
public static final String	PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE	"hn2"
public static final String	PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count_log_norm"
public static final String	PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count_norm"
public static final String	PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE	"otu_count"
public static final String	PIPELINE_PARSER_INPUT_TYPE	"classifier_output"
public static final String	PIPELINE_R_INPUT_TYPE	"R"
public static final String	PIPELINE_SEQ_INPUT_TYPE	"seq"
public static final String	PIPELINE_STATS_TABLE_INPUT_TYPE	"stats"
public static final String	PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE	"taxa_count"

biolockj.util.DemuxUtil

Modifier and Type	Constant Field	Value
public static final String	BARCODE_CUTOFF	"demultiplexer.barcodeCutoff"
public static final String	BARCODE_USE_REV_COMP	"demultiplexer.barcodeRevComp"
public static final String	DEMUX_STRATEGY	"demultiplexer.strategy"
public static final String	MAPPING_FILE	"demultiplexer.mapping"
public static final String	OPTION_BARCODE_IN_HEADER	"barcode_in_header"
public static final String	OPTION_BARCODE_IN_MAPPING	"barcode_in_mapping"
public static final String	OPTION_BARCODE_IN_SEQ	"barcode_in_seq"
public static final String	OPTION_DO_NOT_DEMUX	"do_not_demux"
public static final String	OPTION_ID_IN_HEADER	"id_in_header"

biolockj.util.DockerUtil

Modifier and Type	Constant Field	Value
public static final String	AWS_EFS	"/mnt/efs"
public static final String	AWS_EFS_DB	"/mnt/efs/db"
protected static final String	BLJ_BASH	"blj_bash"
protected static final String	COMPUTE_SCRIPT	"COMPUTE_SCRIPT"
public static final String	CONTAINER_BLJ_DIR	"/app/biolockj"
public static final String	CONTAINER_BLJ_SUP_DIR	"/app/blj_support"
public static final String	CONTAINER_CONFIG_DIR	"/mnt/efs/config"
public static final String	CONTAINER_DB_DIR	"/mnt/efs/db"
public static final String	CONTAINER_INPUT_DIR	"/mnt/efs/input"
public static final String	CONTAINER_META_DIR	"/mnt/efs/metadata"
public static final String	CONTAINER_OUTPUT_DIR	"/mnt/efs/pipelines"
public static final String	CONTAINER_PRIMER_DIR	"/mnt/efs/primer"
protected static final String	DEFAULT_DOCKER_HUB_USER	"biolockj"
protected static final String	DOCKER_HUB_USER	"docker.user"
public static final String	DOCKER_ROOT_HOME	"/root"
protected static final String	SAVE_CONTAINER_ON_EXIT	"docker.saveContainerOnExit"
public static final String	SPAWN_DOCKER_CONTAINER	"spawnDockerContainer"

biolockj.util.DownloadUtil

Modifier and Type	Constant Field	Value
protected static final String	DOWNLOAD_DIR	"pipeline.downloadDir"
public static final String	DOWNLOAD_LIST	"downloadList.txt"

biolockj.util.LogUtil

Modifier and Type	Constant Field	Value
public static final String	USER_PROFILE	"pipeline.userProfile"

biolockj.util.MetaUtil

Modifier and Type	Constant Field	Value
protected static final String	DEFAULT_COL_DELIM	"\t"
protected static final String	DEFAULT_COMMENT_CHAR	""
protected static final String	DEFAULT_NULL_VALUE	"NA"
public static final String	META_BARCODE_COLUMN	"metadata.barcodeColumn"
public static final String	META_COLUMN_DELIM	"metadata.columnDelim"
public static final String	META_COMMENT_CHAR	"metadata.commentChar"
public static final String	META_FILE_PATH	"metadata.filePath"
public static final String	META_FILENAME_COLUMN	"metadata.fileNameColumn"
public static final String	META_NULL_VALUE	"metadata.nullValue"
public static final String	META_REQUIRED	"metadata.required"
public static final String	USE_EVERY_ROW	"metadata.useEveryRow"

biolockj.util.NextflowUtil

Modifier and Type	Constant Field	Value
public static final String	AWS_CONFIG_DIR	"config"
public static final String	AWS_COPY_INPUTS_TO_S3	"aws.copyInputsToS3"
public static final String	AWS_COPY_PIPELINE_TO_S3	"aws.copyPipelineToS3"
public static final String	AWS_COPY_REPORTS_TO_S3	"aws.copyReportsToS3"
public static final String	AWS_DB_DIR	"db"
public static final String	AWS_PIPELINE_DIR	"pipelines"
public static final String	AWS_PURGE_EFS_INPUTS	"aws.purgeEfsInputs"
public static final String	AWS_PURGE_EFS_OUTPUT	"aws.purgeEfsOutput"
public static final String	AWS_RAM	"aws.ram"
public static final String	AWS_REPORT_DIR	"reports"
public static final String	AWS_S3	"aws.s3"
protected static final String	NF_LOG	"/app/biolockj/web_app/.nextflow.log"

biolockj.util.RMetaUtil

Modifier and Type	Constant Field	Value
protected static final String	BINARY_FIELDS	"R_internal.binaryFields"
protected static final String	NUM_META_COLS	"R_internal.numMetaCols"
protected static final String	R_EXCLUDE_FIELDS	"r.excludeFields"
protected static final String	R_MDS_REPORT_FIELDS	"r_PlotMds.reportFields"
protected static final String	R_NOMINAL_FIELDS	"r.nominalFields"
protected static final String	R_NUMERIC_FIELDS	"r.numericFields"
protected static final String	R_REPORT_FIELDS	"r.reportFields"

biolockj.util.RuntimeParamUtil

Modifier and Type	Constant Field	Value
protected static final String	BASE_DIR_FLAG	"b"
protected static final String	CONFIG_DIR_FLAG	"C"
protected static final String	CONFIG_FLAG	"c"
protected static final String	DIRECT_FLAG	"d"
protected static final String	DOCKER_FLAG	"-docker"
protected static final String	HOST_BLJ	"-blj"
protected static final String	HOST_BLJ_SUP	"-bljSup"
protected static final String	HOST_HOME_USER_DIR	"u"
protected static final String	INPUT_DIR_FLAG	"i"
protected static final String	META_DIR_FLAG	"m"
protected static final String	PASSWORD_FLAG	"p"
protected static final String	RESTART_FLAG	"r"

biolockj.util.SeqUtil

Modifier and Type	Constant Field	Value
public static final String	FASTA_HEADER_DEFAULT_DELIM	">"
public static final String	ILLUMINA_FW_READ_IND	" 1:N:"
public static final String	ILLUMINA_RV_READ_IND	" 2:N:"

biolockj.util.TaxaUtil

Modifier and Type	Constant Field	Value
public static final String	NORMALIZED	"norm"
protected static final String	TAXA_TABLE	"taxaCount"