validateBCLSheet: Illumina sample sheet cleaning and updating for bcl2Fastq...

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

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)

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.