From d107727ca687131832837af04a38f2d60800d1cb Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 29 Nov 2015 14:37:15 +0100
Subject: [PATCH] Fix graph issues
---
.../pipelines/flexiprep/Flexiprep.scala | 1 +
.../pipelines/flexiprep/QcCommand.scala | 23 ++++++++++---------
2 files changed, 13 insertions(+), 11 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 1f1f2510c..7c2b9ace1 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -195,6 +195,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
override def beforeGraph(): Unit = {
fqSync.beforeGraph()
+ commands = qcCmdR1.jobs ::: qcCmdR2.jobs ::: fqSync :: Nil
super.beforeGraph()
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 4cb06039b..8eb65f074 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -50,7 +50,15 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val seqtk = new SeqtkSeq(root)
var clip: Option[Cutadapt] = None
var trim: Option[Sickle] = None
- var outputCommand: BiopetCommandLineFunction = null
+ lazy val outputCommand: BiopetCommandLineFunction = if (compress) {
+ val gzip = Gzip(root)
+ gzip.output = output
+ gzip
+ } else {
+ val cat = Cat(root)
+ cat.output = output
+ cat
+ }
def jobs = (Some(seqtk) :: clip :: trim :: Some(outputCommand) :: Nil).flatten
@@ -123,16 +131,9 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
case _ => seqtk.output
}
- if (compress) outputCommand = {
- val gzip = new Gzip(root)
- gzip.output = output
- outputFile :<: gzip
- }
- else outputCommand = {
- val cat = new Cat(root)
- cat.input = outputFile :: Nil
- cat.output = output
- cat
+ outputCommand match {
+ case gzip: Gzip => outputFile :<: gzip
+ case cat: Cat => cat.input = outputFile :: Nil
}
seqtk.beforeGraph()
--
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