From 070a5d81abd11bc0318f4957b7ef418df2f61c40 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Sun, 21 Feb 2021 17:39:45 +0100
Subject: [PATCH] task: add duphold.wdl
---
duphold.wdl | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 75 insertions(+)
create mode 100644 duphold.wdl
diff --git a/duphold.wdl b/duphold.wdl
new file mode 100644
index 0000000..80fe31d
--- /dev/null
+++ b/duphold.wdl
@@ -0,0 +1,75 @@
+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Duphold {
+ input {
+ File inputVcf
+ File bamFile
+ File bamIndex
+ File referenceFasta
+ File referenceFastaFai
+ String sample
+ String outputPath = "./duphold.vcf"
+
+ String memory = "15G"
+ Int timeMinutes = 1440
+ String dockerImage = "quay.io/biocontainers/duphold:0.2.1--h516909a_1"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ export DUPHOLD_SAMPLE_NAME=~{sample}
+ duphold \
+ -v ~{inputVcf} \
+ -b ~{bamFile} \
+ -f ~{referenceFasta} \
+ -o ~{outputPath}
+ }
+
+ output {
+ File outputVcf = outputPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputVcf: {description: "The VCF file to process.", category: "required"}
+ bamFile: {description: "The bam file to process.", category: "required"}
+ bamIndex: {description: "The index of the bam file.", category: "required"}
+ referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
+ referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
+ sample: {description: "The name of the sample.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
+ timeMinutes: {description: "The maximum duration (in minutes) the tool is allowed to run.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputVcf: {description: "Duphold annotated VCF file."}
+ }
+}
--
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