From 9af789ca1234c145fd8e86d78630a9527c4cfe53 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 30 May 2018 09:17:11 +0200
Subject: [PATCH] add makeStarRGline task
---
star.wdl | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/star.wdl b/star.wdl
index 32dd056..92245ec 100644
--- a/star.wdl
+++ b/star.wdl
@@ -47,4 +47,19 @@ task Star {
cpu: select_first([runThreadN, 1])
memory: select_first([memory, 10])
}
-}
\ No newline at end of file
+}
+
+task makeStarRGline {
+ String sample
+ String library
+ String? platform
+ String readgroup
+
+ command {
+ printf '"ID:${readgroup}" "LB:${library}" "PL:${default="ILLUMINA" platform}" "SM:${sample}"'
+ }
+
+ output {
+ String rgLine = read_string(stdout())
+ }
+}
--
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