Commit a278b762 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing stats output file

(cherry picked from commit 54d5384)
parent 75e08dec
...@@ -47,9 +47,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String) ...@@ -47,9 +47,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
val seqtk = new SeqtkSeq(parent) val seqtk = new SeqtkSeq(parent)
var clip: Option[Cutadapt] = if (!flexiprep.skipClip) Some(new Cutadapt(parent, fastqc)) else None var clip: Option[Cutadapt] = if (!flexiprep.skipClip) Some(new Cutadapt(parent, fastqc)) else None
var trim: Option[Sickle] = if (!flexiprep.skipTrim) { var trim: Option[Sickle] = if (!flexiprep.skipTrim) {
val sickle = new Sickle(parent) Some(new Sickle(root))
sickle.outputStats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
Some(sickle)
} else None } else None
lazy val outputCommand: BiopetCommandLineFunction = if (compress) { lazy val outputCommand: BiopetCommandLineFunction = if (compress) {
...@@ -136,6 +134,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String) ...@@ -136,6 +134,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
case Some(c) => c.fastqOutput case Some(c) => c.fastqOutput
case _ => seqtk.output case _ => seqtk.output
} }
t.outputStats = new File(output.getParentFile, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
addPipeJob(t) addPipeJob(t)
} }
...@@ -170,7 +169,6 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String) ...@@ -170,7 +169,6 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
case _ => new BiopetFifoPipe(parent, seqtk :: outputCommand :: Nil) case _ => new BiopetFifoPipe(parent, seqtk :: outputCommand :: Nil)
} }
//val cmds = (Some(seqtk) :: clip :: trim :: Some(new Gzip(root)) :: Nil).flatten
cmd.beforeGraph() cmd.beforeGraph()
cmd.commandLine cmd.commandLine
} }
......
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