From 5b827f8a90d7a0efe2764a6afcf7d23c4fec24fc Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Thu, 2 Apr 2020 16:16:20 +0200
Subject: [PATCH] add smoove.wdl
---
smoove.wdl | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 68 insertions(+)
create mode 100644 smoove.wdl
diff --git a/smoove.wdl b/smoove.wdl
new file mode 100644
index 0000000..93523f3
--- /dev/null
+++ b/smoove.wdl
@@ -0,0 +1,68 @@
+version 1.0
+
+# MIT License
+#
+# 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 CallSV {
+ input {
+ File bamFile
+ File bamIndex
+ File referenceFasta
+ File referenceFastaFai
+ String sample
+ String outputDir = "./smoove"
+
+ String memory = "15G"
+ String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputDir})"
+ smoove call \
+ --outdir ~{outputDir} \
+ --name ~{sample} \
+ --fasta ~{referenceFasta} \
+ ~{bamFile}
+ }
+
+ output {
+ File smooveVcf = outputDir + "/" + sample + "-smoove.vcf.gz"
+ }
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ bamFile: {description: "The bam file to process.", category: "required"}
+ bamIndex: {description: "The index 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" }
+ outputDir: {description: "The location the output VCF file should be written.", category: "common"}
+ sample: {description: "The name of the sample", category: "required"}
+ memory: {description: "The memory required to run the programs", 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"}
+ }
+}
\ No newline at end of file
--
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