Commit ca9c7e5c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix zcat for chunking

parent f4f1f4cb
......@@ -36,7 +36,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
/** Returns command to execute */
def cmdLine = required(executable) +
(if (inputAsStdin) "" else required(input)) +
(if (inputAsStdin) "" else repeat(input)) +
(if (outputAsStsout) "" else " > " + required(output))
}
......
......@@ -253,8 +253,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
throw new IllegalStateException("R1 and R2 file number is not the same")
if (fastq_R1.length > 1) {
add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
val zcat = new Zcat(this)
zcat.input = fastq_R1
add(zcat | new Gzip(this) > fastqR1Qc)
if (paired) {
val zcat = new Zcat(this)
zcat.input = fastq_R2
add(zcat | new Gzip(this) > fastqR2Qc.get)
}
}
outputFiles += ("output_R1_gzip" -> fastqR1Qc)
......
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