validateBCLSheet {basecallQC} | R Documentation

## Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7

### Description

Parses an Illumina bcl2Fastq sample sheet to create a standardised/updated sample sheet for bcl2Fastq >= Version 2.1.7

### Usage

    validateBCLSheet(sampleSheet, param = bcl2fastqparams)

### Arguments

`sampleSheet` | File location of a sample sheet for Illumina basecalling using bcl2Fastq (See vignette for more details).
`param` | A BCL2FastQparams object

### Value

cleanedSampleSheet A data.frame containing the cleaned sample sheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7.

### Author(s)

Thomas Carroll and Marian Dore

### Examples

    fileLocations <- system.file("extdata",package="basecallQC")
    runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
    config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
    sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
    bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
    cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams)

[Package basecallQC version 1.12.0 Index]