A B C D E F G H I J K L M N O P Q R S T U V W X Y

A

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.

A B C D E F G H I J K L M N O P Q R S T U V W X Y