From 48431cd56b9361323c88ae2f8dd03e7a371227b8 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Aug 2014 13:36:43 +0200
Subject: [PATCH] Make Sample and library name required
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 6 ++++--
1 file changed, 4 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 5066375ae..668eaa355 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
@@ -26,10 +26,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
@Argument(doc = "Skip summary", shortName = "skipsummary", required = false)
var skipSummary: Boolean = false
- @Argument(doc = "Sample name", shortName = "sample", required = false)
+ @Argument(doc = "Sample name", shortName = "sample", required = true)
var sampleName: String = _
- @Argument(doc = "Library name", shortName = "library", required = false)
+ @Argument(doc = "Library name", shortName = "library", required = true)
var libraryName: String = _
var paired: Boolean = (input_R2 != null)
@@ -51,6 +51,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (!skipClip) skipClip = config("skipclip", default = false)
if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
+ if (sampleName == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
+ if (libraryName == null) throw new IllegalStateException("Missing Library name on flexiprep module")
else if (!outputDir.endsWith("/")) outputDir += "/"
paired = (input_R2 != null)
--
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