- NAME - Static variable in class biolockj.util.ValidationUtil
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The first column in an expectation file must be "name"
- NAME_PROP - Static variable in class biolockj.module.hello_world.Hello_Friends
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- NAME_PROP - Static variable in class biolockj.module.hello_world.Step3
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- NAME_PROP_DEFAULT - Static variable in class biolockj.module.hello_world.Hello_Friends
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- NAME_PROP_DEFAULT - Static variable in class biolockj.module.hello_world.Step3
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- NAME_PROP_DESC - Static variable in class biolockj.module.hello_world.Hello_Friends
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- NAME_PROP_DESC - Static variable in class biolockj.module.hello_world.Step3
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- newSampleRow(String) - Method in class biolockj.module.report.taxa.TaxaLevelTable
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- nextflowLogExists() - Static method in class biolockj.util.NextflowUtil
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Return true if the Nextflow log has been saved to the pipeline root directory
- NextflowUtil - Class in biolockj.util
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This utility builds the Nextflow main.nf used in AWS pipelines.
- NextflowUtil() - Constructor for class biolockj.util.NextflowUtil
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- NF_LOG - Static variable in class biolockj.util.NextflowUtil
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The Docker container will generate a nextflow.log file in the root directory, this is the file name
- NO_BROAD_USE - Static variable in class biolockj.Properties
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Added description for general properties that are not meant to be used in their general form.
- NO_VERSION - Static variable in interface biolockj.module.BioModule
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- NormalizeByReadsPerMillion - Class in biolockj.module.report.taxa
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Normalize each sample for sequencing depth by reporting each value as the number
of counts per million counts in a given sample.
- NormalizeByReadsPerMillion() - Constructor for class biolockj.module.report.taxa.NormalizeByReadsPerMillion
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- NORMALIZED - Static variable in class biolockj.util.TaxaUtil
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File suffix appended to normalized taxa count tables: "norm"
- NormalizeTaxaTables - Class in biolockj.module.report.taxa
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This utility is used to normalize and/or log-transform the raw OTU counts using the formulas:
Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1
Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ]
The code implementation supports (log_base = e) and (log_base = 10) which is configured via
Constants.REPORT_LOG_BASE property.
- NormalizeTaxaTables() - Constructor for class biolockj.module.report.taxa.NormalizeTaxaTables
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- NUM_ITERATIONS - Static variable in class biolockj.module.report.otu.RarefyOtuCounts
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- NUM_LINES_TEMP_FILE - Static variable in class biolockj.module.implicit.Demultiplexer
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Module splits multiplexed file into smaller files with this number of lines: 2000000
- NUM_MERGED_READS - Static variable in class biolockj.module.seq.PearMergeReads
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Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"
- NUM_META_COLS - Static variable in class biolockj.util.RMetaUtil
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Name of R script variable with metadata column count //TODO: is this an int? or a String giving a variable storing an int ?
- NUM_OTUS - Static variable in class biolockj.module.implicit.parser.ParserModuleImpl
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- NUM_RAREFIED_READS - Static variable in class biolockj.module.seq.RarefySeqs
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Metadata column name for column that holds number of rarefied reads per sample: "Num_Rarefied_Reads"
- NUM_READS - Static variable in class biolockj.module.implicit.RegisterNumReads
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Metadata column name for column that holds number of reads per sample: "Num_Reads"
- NUM_TRIMMED_READS - Static variable in class biolockj.module.seq.TrimPrimers
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Metadata column name for column that holds number of trimmed reads per sample: "Num_Trimmed_Reads"
- NUM_VALID_READS - Static variable in class biolockj.module.seq.SeqFileValidator
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Column name that holds number of valid reads per sample: "Num_Valid_Reads"
- NUMERTIC_TYPE - Static variable in class biolockj.Properties
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