From 264627ed6d4cc563f0173b436723d9c440f63735 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 16:15:44 +0200
Subject: [PATCH] add samtools application
---
samtools.wdl | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/samtools.wdl b/samtools.wdl
index a1192ac..ecff136 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -117,3 +117,31 @@ task fastq {
}
}
+
+task view {
+ String? preCommand
+ File inFile
+ File? referenceFasta
+ String? outputFileName
+ Boolean? outputBam
+ Boolean? uncompressedBamOutput
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Int? threads
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ samtools view \
+ ${"-T " + referenceFasta} \
+ ${"-o " + outputFileName} \
+ ${true="-b " false="" outputBam} \
+ ${true="-u " false="" uncompressedBamOutput} \
+ ${"-f " + includeFilter} \
+ ${"-F " + excludeFilter} \
+ ${"-G " + excludeSpecificFilter} \
+ ${"--threads " + threads - 1} \
+ ${inFile}
+ }
+}
--
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