Merge pull request #210 from biowdl/addSmoove

Add smoove

CHANGELOG.md

@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 -->
 version 3.1.0
 ---------------------------
++ Add WDL task for smoove (lumpy) sv-caller.
 + Default threads for BWA in bwa.Kit task: 4. Samtools sort in the
   same task: 1. Output BAM compression level to 1.
 + Lima: Add missing output to parameter_meta.

smoove.wdl

+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 Call {
+    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"
+        Int timeMinutes = 1440
+    }
+
+    command {
+        set -e
+        mkdir -p ~{outputDir}
+        smoove call \
+        --outdir ~{outputDir} \
+        --name ~{sample} \
+        --fasta ~{referenceFasta} \
+        ~{bamFile}
+    }
+
+    output {
+        File smooveVcf = outputDir + "/" + sample + "-smoove.vcf.gz"
+    }
+
+    runtime {
+        memory: memory
+        docker: dockerImage
+        time_minutes: timeMinutes
+
+    }
+
+    parameter_meta {
+        # inputs
+        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" }
+        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"}
+        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"}
+    }
+}