From d61425278925d42b5d9ab5c2fe655130e5444c58 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 27 Oct 2015 16:39:24 +0100
Subject: [PATCH] Quick fix, error in the HelloPipeline
---
.../scala/org/example/group/pipelines/HelloPipeline.scala | 8 +++-----
1 file changed, 3 insertions(+), 5 deletions(-)
diff --git a/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
index cd4a158c1..e7df3db17 100644
--- a/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
+++ b/external-example/src/main/scala/org/example/group/pipelines/HelloPipeline.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet/pipelines.mypipeline
+package nl.lumc.sasc.biopet.pipelines.mypipeline
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
@@ -29,10 +29,8 @@ class HelloPipeline(val root: Configurable) extends QScript with SummaryQScript
val fastqc = new Fastqc(this)
fastqc.fastqfile = config("fastqc_input")
- fastqc.output = new File(outputDir,
-
- /* Only required when using [[SummaryQScript]] */
- addSummaryQScript(shiva)
+ fastqc.output = new File(outputDir, "fastqc.txt")
+ add(fastqc)
// From here you can use the output files of shiva as input file of other jobs
}
--
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