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A

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

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.

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

addSummaryFooterForFailedPipeline(String) - 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

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"

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"

APP_START_TIME - Static variable in class biolockj.Constants

Captures the application start time

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_CONFIG_DIR - Static variable in class biolockj.util.NextflowUtil

Name of the AWS S3 sub-directory used to save pipeline reports

AWS_COPY_INPUTS_TO_S3 - Static variable in class biolockj.util.NextflowUtil

Config Boolean property: If enabled save all input files to S3: "aws.copyInputsToS3"

AWS_COPY_PIPELINE_TO_S3 - Static variable in class biolockj.util.NextflowUtil

Config Boolean property: If enabled save pipeline to S3: "aws.copyPipelineToS3"

AWS_COPY_REPORTS_TO_S3 - Static variable in class biolockj.util.NextflowUtil

Config Boolean property: If enabled save reports to S3: "aws.copyPipelineToS3"

AWS_DB_DIR - Static variable in class biolockj.util.NextflowUtil

Name of the AWS S3 sub-directory used to save pipeline reports

AWS_EFS - Static variable in class biolockj.util.DockerUtil

Docker container root user EFS directory

AWS_EFS_DB - Static variable in class biolockj.util.DockerUtil

Docker container root user DB directory

AWS_PIPELINE_DIR - Static variable in class biolockj.util.NextflowUtil

Name of the AWS S3 sub-directory used to save pipeline reports

AWS_PURGE_EFS_INPUTS - Static variable in class biolockj.util.NextflowUtil

Config Boolean property: If enabled delete all EFS dirs (except pipelines): "aws.purgeEfsInputs"

AWS_PURGE_EFS_OUTPUT - Static variable in class biolockj.util.NextflowUtil

Config Boolean property: If enabled delete all EFS/pipelines: "aws.purgeEfsOutput"

AWS_RAM - Static variable in class biolockj.util.NextflowUtil

Config String property: AWS memory set in Nextflow main.nf: "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 pipeline output directory used by Nextflow main.nf: "aws.s3"

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 $EFS_META/testMetadata.tsv s3://blj-2019-04-05/metadata/testMetadata.tsv

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