From 4154cee8a96444748322c811ef01fe78557d2430 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 19 Mar 2020 14:41:58 +0100
Subject: [PATCH] rename outputBAM back to outputBam, remove boolean
---
samtools.wdl | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index de7f2a3..cc106d3 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -336,7 +336,6 @@ task View {
File? referenceFasta
String outputFileName = "view.bam"
Boolean includeHeader = false
- Boolean outputBam = false
Boolean uncompressedBamOutput = false
Int? includeFilter
Int? excludeFilter
@@ -356,7 +355,6 @@ task View {
samtools view -b \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
- ~{true="-b " false="" outputBam} \
~{true="-u " false="" uncompressedBamOutput} \
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
@@ -368,7 +366,7 @@ task View {
}
output {
- File outputBAM = outputFileName
+ File outputBam = outputFileName
File outputBamIndex = outputIndexPath
}
--
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