From a80da1d97ee587ee563a77175dfee0b559cdae80 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 21 Apr 2020 10:44:54 +0200
Subject: [PATCH] Reinstate symlink.
---
picard.wdl | 2 +-
samtools.wdl | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 5a75924..5393cd3 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -334,7 +334,7 @@ task CreateSequenceDictionary {
}
output {
- File outputDict = outputDir + "/" + basename(InputFile) + ".dict"
+ File outputDict = outputDir + "/" + basename(inputFile) + ".dict"
}
runtime {
diff --git a/samtools.wdl b/samtools.wdl
index 15ea9a2..24ae7f9 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -70,7 +70,7 @@ task Faidx {
command {
set -e
mkdir -p "~{outputDir}"
- ln ~{inputFile} "~{outputDir}/~{basenameInputFile}"
+ ln -s ~{inputFile} "~{outputDir}/~{basenameInputFile}"
samtools faidx \
"~{outputDir}/~{basenameInputFile}"
}
--
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