From 6090fa335d4a665d9bcdc99b5a2667ed42a5bf0e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 26 Jun 2014 10:29:25 +0200
Subject: [PATCH] fixed call to sub pipeline
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 3 ++-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 112da3f3c..b7b9e3b3a 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -231,7 +231,7 @@ class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
if (filename.endsWith(".gzip")) filename = filename.substring(0,filename.size - 5)
if (filename.endsWith(".fastq")) filename = filename.substring(0,filename.size - 6)
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
- fastqcCommand.output = outDir + "/" + filename + "_fastqc.ouput"
+ fastqcCommand.output = outDir + "/" + filename + "_fastqc.output"
fastqcCommand.afterGraph
add(fastqcCommand)
return fastqcCommand
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index aaf4fe352..d67b4fa80 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -109,7 +109,8 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.outputDir = outputDir + "flexiprep/"
- flexiprep.script
+ flexiprep.init
+ flexiprep.biopetScript
addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
fastq_R1 = flexiprep.outputFiles("output_R1")
if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")
--
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