From daf3d59195c816ee3d2074b83a7d230170ba7666 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 3 Feb 2015 16:31:26 +0100
Subject: [PATCH] Expose Flexiprep sampleId and libraryId back to the command
line
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index db5c638fd..c8cb6f6a6 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -38,10 +38,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
/** Skip Clip fastq files */
var skipClip: Boolean = config("skip_clip", default = false)
+ // TODO: hide sampleId and libraryId from the command line so they do not interfere with our config values
+
/** Sample name */
+ @Argument(doc = "Sample ID", shortName = "sample", required = true)
var sampleId: String = _
/** Library name */
+ @Argument(doc = "Library ID", shortName = "library", required = true)
var libraryId: String = _
var paired: Boolean = (input_R2 != null)
--
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