# pipeline.R
# do the A to Z alignment pipeline on a sample
`pipeline` <- function( sampleID=NULL, annotationFile="Annotation.txt", optionsFile="Options.txt", ...) {
checkSampleNames( sampleID)
datatype <- getAnnotationValue( annotationFile, key=sampleID, columnArg="DataType", notfound="RNA-seq")
if ( datatype == "RNA-seq") {
ans <- pipe.RNAseq( sampleID, annotationFile, optionsFile, ...)
} else if ( datatype == "DNA-seq") {
ans <- pipe.DNAseq( sampleID, annotationFile, optionsFile, ...)
} else if ( datatype == "ChIP-seq") {
ans <- pipe.ChIPseq( sampleID, annotationFile, optionsFile, ...)
} else if ( datatype == "RIP-seq") {
ans <- pipe.RIPseq( sampleID, annotationFile, optionsFile, ...)
} else {
cat( "\nInvalid DuffyNGS data type: ", datatype)
cat( "\nValid types: RNA-seq, DNA-seq, ChIP-seq, RIP-seq \n")
stop()
}
return( ans)
}
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