Commit 81188921 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing BIOPET-487

parent 2221fa53
......@@ -262,11 +262,15 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (fastq_R1.length > 1) {
val zcat = new Zcat(this)
zcat.input = fastq_R1
add(zcat | new Gzip(this) > fastqR1Qc)
val cmdR1 = zcat | new Gzip(this) > fastqR1Qc
cmdR1.isIntermediate = !keepQcFastqFiles
add(cmdR1)
if (paired) {
val zcat = new Zcat(this)
zcat.input = fastq_R2
add(zcat | new Gzip(this) > fastqR2Qc.get)
val cmdR2 = zcat | new Gzip(this) > fastqR2Qc.get
cmdR2.isIntermediate = !keepQcFastqFiles
add(cmdR2)
}
}
......
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