From de43e51b5a4e0659c62185be8f0883daba842ff2 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jul 2019 16:35:04 +0200
Subject: [PATCH] small fixes
---
gatk.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index a8b1a07..241fbf2 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -32,7 +32,7 @@ task ApplyBQSR {
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
- ~{true="-L" false="" defined(sequenceGroupInterval)} ~{sep=" -L " select_first([sequenceGroupInterval], [])}
+ ~{true="-L" false="" defined(sequenceGroupInterval)} ~{sep=" -L " select_first([sequenceGroupInterval, []])}
}
output {
@@ -82,7 +82,7 @@ task BaseRecalibrator {
--use-original-qualities \
-O ~{recalibrationReportPath} \
--known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
- ~{true="-L" false="" defined(sequenceGroupInterval)} ~{sep=" -L " select_first([sequenceGroupInterval], [])}
+ ~{true="-L" false="" defined(sequenceGroupInterval)} ~{sep=" -L " select_first([sequenceGroupInterval, []])}
}
output {
--
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