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activeIndicator - Static variable in class biolockj.launch.ProgressUtil
 
addBadFilesToSummary() - Method in class biolockj.module.seq.TrimPrimers
Update summaryMsgs with list of seq files that contained no reads with a valid primer.
addColumn(String, Map<String, String>, File, boolean) - Static method in class biolockj.util.MetaUtil
Adds a column to the metadata file.
addCount(Long) - Method in class biolockj.node.JsonNode
Add taxa count
addGeneralProperty(String) - Method in class biolockj.module.BioModuleImpl
 
addGeneralProperty(String, String) - Method in class biolockj.module.BioModuleImpl
 
addGeneralProperty(String, String, String) - Method in class biolockj.module.BioModuleImpl
 
addHitRatioToMetadata() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables
Add Num_Hits/Num_Reads as Hit_Ratio column to the metadata file
addLeadingSpaces(String, int) - Static method in class biolockj.util.BioLockJUtil
Add leading spaces until the val is padded to given length
AddMetadataToPathwayTables - Class in biolockj.module.report.humann2
This BioModule is used to add metadata columns to the HumanN2 pathway abundance, pathway coverage, and gene family tables.
AddMetadataToPathwayTables() - Constructor for class biolockj.module.report.humann2.AddMetadataToPathwayTables
 
AddMetadataToTaxaTables - Class in biolockj.module.report.taxa
This BioModule is used to add metadata columns to the OTU abundance tables.
AddMetadataToTaxaTables() - Constructor for class biolockj.module.report.taxa.AddMetadataToTaxaTables
 
addMissingFields() - Method in class biolockj.module.implicit.qiime.BuildQiimeMapping
Create QIIME mapping based on metadata file, output to temp dir.
addNewProperty(String, String, String) - Method in class biolockj.module.BioModuleImpl
 
addNewProperty(String, String, String, String) - Method in class biolockj.module.BioModuleImpl
 
addNode(OtuNode) - Method in class biolockj.node.ParsedSample
Add the OtuNode to the ParsedSample.
addOtuNode(OtuNode) - Method in interface biolockj.module.implicit.parser.ParserModule
Each sample with taxonomic assignments from a ClassifierModule is parsed by ParserModule.parseSamples() to produce a ParsedSample.
addOtuNode(OtuNode) - Method in class biolockj.module.implicit.parser.ParserModuleImpl
 
addOtuNode(OtuNode) - Method in class biolockj.module.implicit.parser.wgs.KrakenParser
 
addParsedSample(ParsedSample) - Method in class biolockj.module.implicit.parser.ParserModuleImpl
Add ParsedSample to parser cache
AddPseudoCount - Class in biolockj.module.report.taxa
 
AddPseudoCount() - Constructor for class biolockj.module.report.taxa.AddPseudoCount
 
addSummaryFooterForFailedPipeline() - Static method in class biolockj.util.SummaryUtil
Called when pipeline fails to add summary details to summary file, if possible.
addTaxa(String, String) - Method in interface biolockj.node.OtuNode
Add OtuNode taxa names for the Config."report.taxonomyLevels" level mapped by the classifier specific levelDelim parameter: .
addTaxa(String, String) - Method in class biolockj.node.OtuNodeImpl
If called for level not included in Config."report.taxonomyLevels", check if the top level taxonomy level is already assigned.
addTrailingSpaces(String, int) - Static method in class biolockj.util.BioLockJUtil
Add trailing spaces until the val is padded to given length
addValue(String, String, Double) - Method in class biolockj.module.report.taxa.TaxaLevelTable
 
ADJ_PVAL_ATTRIBUTE - Static variable in class biolockj.module.report.r.R_CalculateStats
This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "ATTRIBUTE"
ADJ_PVAL_GLOBAL - Static variable in class biolockj.module.report.r.R_CalculateStats
This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "GLOBAL"
ADJ_PVAL_LOCAL - Static variable in class biolockj.module.report.r.R_CalculateStats
This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "LOCAL"
ADJ_PVAL_TAXA - Static variable in class biolockj.module.report.r.R_CalculateStats
This "r_CalculateStats.pAdjustMethod" option can be set in Config file: "TAXA"
allFlags - Static variable in class biolockj.pipelines.PipelineUtil
 
allTaxonomyLevels() - Static method in class biolockj.util.TaxaUtil
Returns a list of all taxonomy levels, not only the levels configured via Config."report.taxonomyLevels".
ALPHA_DIV_NULL_VALUE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
Value output by "alpha_diversity.py" for null values: "N/A"
ALPHA_DIVERSITY_TABLE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
File produced by QIIME "alpha_diversity.py" script: "alphaDiversity.txt"
anim - Static variable in class biolockj.launch.LabeledSpinner
 
API_Exception - Exception in biolockj.api
 
API_Exception(String) - Constructor for exception biolockj.api.API_Exception
 
ApiModule - Interface in biolockj.api
 
APP_START_TIME - Static variable in class biolockj.Constants
Captures the application start time
asInnerPath(String) - Method in class biolockj.util.paths.BasicDockerMapper
 
asInnerPath(String) - Method in interface biolockj.util.paths.DockerMountMapper
Convert path to inner path form.
asInnerPath(String) - Method in interface biolockj.util.paths.PathMapper
Convert path to inner path form.
asOuterPath(String) - Method in class biolockj.util.paths.BasicDockerMapper
 
asOuterPath(String) - Method in interface biolockj.util.paths.DockerMountMapper
Convert path to outer path form.
asOuterPath(String) - Method in interface biolockj.util.paths.PathMapper
Convert path to outer path form.
asPipeline(File) - Static method in class biolockj.pipelines.OtherPipelineFactory
 
ASSIGN_ALIAS - Static variable in class biolockj.Constants
The key string to define an alias for an individual module: {@value
assignMainArg() - Method in class biolockj.launch.LaunchProcess
 
AwkFastaConverter - Class in biolockj.module.seq
This BioModule uses awk and gzip to convert input sequence files into a decompressed fasta file format.
AwkFastaConverter() - Constructor for class biolockj.module.seq.AwkFastaConverter
 
AWS_ARG - Static variable in class biolockj.launch.LaunchProcess
 
AWS_CONFIG_DIR - Static variable in class biolockj.util.NextflowUtil
Name of the AWS S3 sub-directory used to save pipeline reports
AWS_COPY_DB_TO_S3 - Static variable in class biolockj.util.NextflowUtil
Config Boolean property:"aws.copyDbToS3"
AWS_COPY_PIPELINE_TO_S3 - Static variable in class biolockj.util.NextflowUtil
Config Boolean property: "aws.copyPipelineToS3"
AWS_COPY_REPORTS_TO_S3 - Static variable in class biolockj.util.NextflowUtil
Config Boolean property: "aws.copyPipelineToS3"
AWS_EC2_HOME - Static variable in class biolockj.util.DockerUtil
Docker container dir to map HOST $HOME to save logs + find Config values using $HOME: "/home/ec2-user" Need to name this dir = "/home/ec2-user" so Nextflow config is same inside + outside of container
AWS_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
Config AWS end parameter switch: "-aws"
AWS_PURGE_EFS_INPUTS - Static variable in class biolockj.util.NextflowUtil
Config Boolean property: "aws.purgeEfsInputs"
AWS_PURGE_EFS_OUTPUT - Static variable in class biolockj.util.NextflowUtil
Config Boolean property: "aws.purgeEfsOutput"
AWS_RAM - Static variable in class biolockj.util.NextflowUtil
Config String property: "aws.ram"
AWS_REPORT_DIR - Static variable in class biolockj.util.NextflowUtil
Name of the AWS S3 subdirectory used to save pipeline reports
AWS_S3 - Static variable in class biolockj.util.NextflowUtil
Config String property: "aws.s3"
AWS_S3_XFER_TIMEOUT - Static variable in class biolockj.Constants
Config Integer property: "aws.s3TransferTimeout"
awsSyncS3(String, boolean) - Static method in class biolockj.util.NextflowUtil
Sync file or directory with S3 bucket.
Dir example: aws s3 sync $EFS/config s3://blj-2019-04-05/config
File example: aws s3 cp ${BLJ_META}/testMetadata.tsv s3://blj-2019-04-05/metadata/testMetadata.tsv Register each efsPath to avoid syncing the same path more than once.
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