From f22018dfe8d283e3a945de0560f0986fcc90f74b Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 5 Apr 2018 15:42:56 +0200
Subject: [PATCH] link instead of merge if one bam file
---
common.wdl | 13 +++++++++++++
samtools.wdl | 7 ++++++-
2 files changed, 19 insertions(+), 1 deletion(-)
diff --git a/common.wdl b/common.wdl
index a780747..79be387 100644
--- a/common.wdl
+++ b/common.wdl
@@ -102,4 +102,17 @@ task appendToStringArray {
runtime {
memory: 1
}
+}
+
+task createLink {
+ File inputFile
+ String outputPath
+
+ command {
+ ln -sf ${inputFile} ${outputPath}
+ }
+
+ output {
+ File link = outputPath
+ }
}
\ No newline at end of file
diff --git a/samtools.wdl b/samtools.wdl
index 4dd5e29..249143f 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -21,7 +21,12 @@ task Merge {
command {
set -e -o pipefail
${preCommand}
- samtools merge ${outputBamPath} ${sep=' ' bamFiles}
+ if [ ${length(bamFiles)} -gt 1 ]
+ then
+ samtools merge ${outputBamPath} ${sep=' ' bamFiles}
+ else
+ ln -sf ${bamFiles} ${outputBamPath}
+ fi
}
output {
--
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