From 45200c5576e1c7061070043213044a694920e722 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 17:11:46 +0100
Subject: [PATCH] Make input and output required
---
.../nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index b91aaafae..159ad4153 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -13,10 +13,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
- @Input
+ @Input(doc="", required = true)
var bamFile: File = _
- @Output
+ @Output(doc="", required = true)
var bigWigFile: File = _
def init(): Unit = {
@@ -33,6 +33,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
igvCount.input = bamFile
igvCount.genomeChromSizes = bs.chromSizesFile
igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
+ add(igvCount)
val wigToBigWig = new WigToBigWig(this)
wigToBigWig.inputWigFile = igvCount.wig.get
--
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