Merge pull request #188 from biowdl/addVT

Add vt

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 2.2.0-dev
 ---------------------------
++ Add vt task for variants normalization and decomposition.
 + Update WDL task Picard (Add task RenameSample)
 + Update WDL task Samtools (Add task FilterShortReadsBam)
 + Add WDL task for BCFtools (bcf to vcf)

vt.wdl

+version 1.0
+
+# Copyright (c) 2020 Sequencing Analysis Support Core - 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 Normalize {
+    input {
+        File inputVCF
+        File inputVCFIndex
+        File referenceFasta
+        File referenceFastaFai
+        String outputPath = "./vt/normalized_decomposed.vcf"
+        String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
+        String memory = "4G"
+    }
+
+    command {
+        set -e
+        mkdir -p "$(dirname ~{outputPath})"
+        vt normalize ~{inputVCF} -r ~{referenceFasta} | vt decompose -s - -o ~{outputPath}
+    }
+
+    output {
+        File outputVcf = outputPath
+    }
+
+    runtime {
+        memory: memory
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        # inputs
+        inputVCF: {description: "The VCF file to process.", category: "required"}
+        inputVCFIndex: {description: "The index of the VCF file to be processed.", category: "required"}
+        outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+        referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+        referenceFastaFai: {description: "The index for the reference fasta file.", 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"}
+    }
+}
+