From 85898c4d4ea63f6323a69d4a4d5f9ec7472d020d Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Thu, 13 Sep 2018 11:04:26 +0200
Subject: [PATCH] Dynamic index searching
---
samtools.wdl | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index ff2daf0..0d43015 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -36,11 +36,10 @@ task Index {
}
output {
+ File index = select_first(flatten([[bamIndexPath], glob(sub(basename(bamFile), "\.bam$", "") + "*.bai")]))
IndexedBamFile outputBam = object {
file: bamFile,
- index: if defined(bamIndexPath)
- then select_first([bamIndexPath])
- else bamFile + ".bai"
+ index: index
}
}
}
--
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