tests/testthat/test_Run2.R

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

library(basecallQC)
context("Test 2nd Run example")
fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(file.path(fileLocations,"Runs/170217_D00467_0227_ACADN3ANXX/"),pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
sampleSheet <- dir(file.path(fileLocations,"Runs/170217_D00467_0227_ACADN3ANXX/"),pattern="*\\.csv",full.names=TRUE)
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)

#'


expect_that(length(unique(bclQC@cleanedSampleSheet$Sample_Project)) ==
                     length(levels(read.delim(sampleSheet,header=T,sep=",",stringsAsFactors = TRUE)$Project)),
                     is_true()
            )