- 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
-
- 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
-
- 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
-
- addTaxa(String, String) - Method in class biolockj.node.OtuNodeImpl
-
- 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
-
- ADJ_PVAL_GLOBAL - Static variable in class biolockj.module.report.r.R_CalculateStats
-
- ADJ_PVAL_LOCAL - Static variable in class biolockj.module.report.r.R_CalculateStats
-
- ADJ_PVAL_TAXA - Static variable in class biolockj.module.report.r.R_CalculateStats
-
- allFlags - Static variable in class biolockj.pipelines.PipelineUtil
-
- allTaxonomyLevels() - Static method in class biolockj.util.TaxaUtil
-
- ALPHA_DIV_NULL_VALUE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- ALPHA_DIVERSITY_TABLE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- 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
-
- 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.