module.implicit

biolockj.module.implicit modules are added to BioLockJ pipelines automatically if needed.
Implicit modules are ignored if included in the Config file unless project.allowImplicitModules=Y

This package contains the following sub-packages:

1. module.implicit.parser contains ParserModule interface & ParserModuleImpl superclass.
2. module.implicit.parser.r16s contains 16S parser modules.
3. module.implicit.parser.wgs contains WGS parser modules.
4. module.implicit.qiime contains QIIME Script wrappers.

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Demultiplexer

(added by BioLockJ) #BioModule biolockj.module.implicit.ImportMetadata

Description: Demultiplex samples into separate files for each sample.

Options:

• demultiplexer.barcodeCutoff
• demultiplexer.barcodeRevComp
• demultiplexer.strategy
• metadata.filePath

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ImportMetadata

(added by BioLockJ) #BioModule biolockj.module.implicit.ImportMetadata

Description: Required 1st module in every pipeline.
If metadata.filePath is undefined, a new metadata file will be created with only a single column "SAMPLE_ID".
The imported file is converted to required BioLockJ metadata format: tab-delimited, with unique column headers, and empty cells are now populated with metadata.nullValue or "NA" if undefined.

Options:

• metadata.columnDelim
• metadata.commentChar
• metadata.filePath
• metadata.nullValue

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RegisterNumReads

(added by BioLockJ) #BioModule biolockj.module.implicit.RegisterNumReads

Description: Add "Num_Reads" column to metadata file to document the total number of reads per sample.

Options:

• report.numReads

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