Commit 8cf28116 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed bug on single end runs

parent 6887ab44
......@@ -68,7 +68,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (paired) runTrimClip(outputFiles("fastq_input_R1"), outputFiles("fastq_input_R2"), outputDir)
else runTrimClip(outputFiles("fastq_input_R1"), outputDir)
runFinalize(List(outputFiles("output_R1")), List(outputFiles("output_R2")))
runFinalize(List(outputFiles("output_R1")), if (outputFiles.contains("output_R2")) List(outputFiles("output_R2")) else List())
}
def runInitialFastqc() {
......@@ -177,7 +177,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
def runFinalize(fastq_R1:List[File], fastq_R2:List[File]) {
if (fastq_R1.length != fastq_R2.length) throw new IllegalStateException("R1 and R2 file number is not the same")
if (fastq_R1.length != fastq_R2.length && paired) throw new IllegalStateException("R1 and R2 file number is not the same")
var R1: File = ""
var R2: File = ""
if (fastq_R1.length == 1) {
......
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