Description Usage Arguments Value Author(s) Examples
View source: R/processIlluminaSamplesheets_Functions.R
Parses an Illumina bcl2Fastq sample sheet to create a standardised/updated sample sheet for bcl2Fastq >= Version 2.1.7
1 | validateBCLSheet(sampleSheet, param = bcl2fastqparams)
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sampleSheet |
File location of a sample sheet for Illumina basecalling using bcl2Fastq (See vignette for more details). |
param |
A BCL2FastQparams object |
cleanedSampleSheet A data.frame containing the cleaned sample sheet for Illumina basecalling using bcl2Fastq versions >= 2.1.7.
Thomas Carroll and Marian Dore
1 2 3 4 5 6 | 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)
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