From 1a80829e5bc6b9f607d3cb748f7af6c47e90f8bf Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 13 Jan 2023 16:37:32 +0100
Subject: [PATCH] Add targets file input to samtools view
---
samtools.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/samtools.wdl b/samtools.wdl
index 587a53f..8503777 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -571,6 +571,7 @@ task View {
Int? excludeFilter
Int? excludeSpecificFilter
Int? MAPQthreshold
+ File? targetFile
Int threads = 1
String memory = "1GiB"
@@ -593,6 +594,7 @@ task View {
~{"-G " + excludeSpecificFilter} \
~{"-q " + MAPQthreshold} \
~{"--threads " + (threads - 1)} \
+ ~{"--target-file " + targetFile} \
~{inFile}
samtools index ~{outputFileName} ~{outputIndexPath}
}
--
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