From 358c946dc86024324455193032d53873b8361d33 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 30 Jun 2022 16:36:09 +0200
Subject: [PATCH] fix duoble .bgz and and index to output
---
gridss.wdl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/gridss.wdl b/gridss.wdl
index c12c24d..38daa02 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -90,7 +90,9 @@ task AnnotateSvTypes {
Int timeMinutes = 240
}
- String index = if sub(outputPath, "\\.bgz", "") != outputPath then "T" else "F"
+ String effectiveOutputPath = sub(outputPath, "\\.bgz", "")
+ String index = if effectiveOutputPath != outputPath then "T" else "F"
+
# Based on https://github.com/PapenfussLab/gridss/issues/74
command <<<
@@ -101,7 +103,7 @@ task AnnotateSvTypes {
library(StructuralVariantAnnotation)
vcf_path <- "~{gridssVcf}"
- out_path <- "~{outputPath}"
+ out_path <- "~{effectiveOutputPath}"
# Simple SV type classifier
simpleEventType <- function(gr) {
@@ -123,6 +125,7 @@ task AnnotateSvTypes {
output {
File vcf = outputPath
+ File? vcfIndex = outputPath + ".tbi"
}
runtime {
--
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