From f941cb35b0194ea6da2250a6b1bf98c1b35d8787 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 2 Feb 2016 13:38:22 +0100
Subject: [PATCH] Added md5 check to pipeline
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 3 +++
1 file changed, 3 insertions(+)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index ba29af9d5..37c6f110a 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -1,5 +1,6 @@
package nl.lumc.sasc.biopet.pipelines.gears
+import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
import nl.lumc.sasc.biopet.extensions.tools.MergeOtuMaps
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Ln }
@@ -107,6 +108,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */
protected def addJobs(): Unit = {
+ inputFiles :+= InputFile(flexiprep.input_R1, config("R1_md5"))
+ flexiprep.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
add(flexiprep)
gs.fastqR1 = Some(flexiprep.fastqR1Qc)
--
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