Commit 6bad7eaf authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed single-end runs

parent 41857e5d
...@@ -172,7 +172,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -172,7 +172,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Adds all chunkable jobs of flexiprep */ /** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File, chunkarg: String): (File, Option[File], List[File]) = { def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File, chunkarg: String): (File, Option[File], List[File]) = {
val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_" val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_"
var results: Map[String, File] = Map()
var R1 = R1_in var R1 = R1_in
var R2 = R2_in var R2 = R2_in
...@@ -181,9 +180,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with ...@@ -181,9 +180,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
val qcCmdR1 = new QcCommand(this, fastqc_R1) val qcCmdR1 = new QcCommand(this, fastqc_R1)
qcCmdR1.input = R1_in qcCmdR1.input = R1_in
qcCmdR1.read = "R1" qcCmdR1.read = "R1"
qcCmdR1.output = if (paired) qcCmdR1.output = if (paired) new File("/dev/stdout")
new File("/dev/stdout") else fastqR1Qc
else new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.fq.gz")
qcCmdR1.isIntermediate = paired || !keepQcFastqFiles qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
if (paired) { if (paired) {
......
...@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman ...@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
super.beforeGraph() super.beforeGraph()
require(read != null) require(read != null)
deps ::= output deps ::= input
} }
override def defaultCoreMemory = 2.0 override def defaultCoreMemory = 2.0
......
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