tests/testthat/test_Run1.R

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

library(basecallQC)
context("Test first Run example")
fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/"),pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
sampleSheet <- dir(file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/"),pattern="*\\.csv",full.names=TRUE)
outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
plot <- passFilterBoxplot(bclQC,groupBy = "Sample")
expect_that(class(plot)[2] == "ggplot",
            is_true()
)