From d09f9f9dd2f9d9692243273e7e89cfcd9082b418 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <sajvanderzeeuw@sasc-sander.lumcnet.prod.intern>
Date: Tue, 28 Oct 2014 11:52:42 +0100
Subject: [PATCH] make intermediate fastq
---
.../nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index b05aae0f0..9cd93a32d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -171,8 +171,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
if (config("bam_to_fastq", default = false).getBoolean) {
- val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + runID + ".R1.fastq", runDir + sampleID + "-" + runID + ".R2.fastq")
- add(samToFastq)
+ val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + runID + ".R1.fastq",
+ runDir + sampleID + "-" + runID + ".R2.fastq")
+ add(samToFastq, isIntermediate = true)
val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir, startJobs = false)
mapping.input_R1 = samToFastq.fastqR1
mapping.input_R2 = samToFastq.fastqR2
--
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