From 4e2a09e11c36a69b84451c44bf70c50825d67746 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 30 Jun 2022 15:57:39 +0200
Subject: [PATCH] detect if compressed
---
gridss.wdl | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gridss.wdl b/gridss.wdl
index d0428e5..c12c24d 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -90,6 +90,8 @@ task AnnotateSvTypes {
Int timeMinutes = 240
}
+ String index = if sub(outputPath, "\\.bgz", "") != outputPath then "T" else "F"
+
# Based on https://github.com/PapenfussLab/gridss/issues/74
command <<<
set -e
@@ -115,7 +117,7 @@ task AnnotateSvTypes {
gr <- breakpointRanges(vcf)
svtype <- simpleEventType(gr)
info(vcf[gr$sourceId])$SVTYPE <- svtype
- writeVcf(vcf, out_path, index=T)
+ writeVcf(vcf, out_path, index=~{index})
EOF
>>>
--
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