Description Usage Arguments Value Author(s) Examples
Creates the command to be used for basecalling/demultiplexing with bcl2fastq versions >= 2.1.7
1 | createBCLcommand(bcl2fastqparams, cleanedSampleSheet, baseMasks)
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bcl2fastqparams |
A BCL2FastQparams object. |
cleanedSampleSheet |
Data.frame of cleaned samplesheet for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7 (see vignette for more details) |
baseMasks |
A data.frame of basemasks as created by createBasemasks() function |
A character vector containing the command for Illumina basecalling using bcl2fastq versions >= 2.1.7
Thomas Carroll and Marian Dore
1 2 3 4 5 6 7 8 9 | 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)
baseMasks <- createBasemasks(cleanedSampleSheet,param=bcl2fastqparams)
toSubmit <- createBCLcommand(bcl2fastqparams,cleanedSampleSheet,baseMasks)
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