add task for peach

peach.wdl

+version 1.0
+
+# Copyright (c) 2021 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 Peach {
+    input {
+        File transcriptTsv
+        File germlineVcf
+        File germlineVcfIndex
+        File tumorName
+        File normalName
+        String outputDir = "./peach"
+        File panelJson
+
+        String memory = "8G"
+        String dockerImage = "quay.io/biowdl/peach:v1.0"
+        Int timeMinutes = 20
+    }
+
+    command {
+        peach \
+        --recreate_bed \
+        --transcript_tsv ~{transcriptTsv} \
+        ~{germlineVcf} \
+        ~{tumorName} \
+        ~{normalName} \
+        1.0 \
+        ~{outputDir} \
+        ~{panelJson} \
+        vcftools
+    }
+
+    output {
+        File callsTsv = "~{outputDir}/~{tumorName}.peach.calls.tsv"
+        File filteredVcf = "~{outputDir}/~{tumorName}.peach.filtered.vcf"
+        File genotypeTsv = "~{outputDir}/~{tumorName}.peach.genotype.tsv"
+        Array[File] peachFiles = [callsTsv, filterVcf, genotypeTsv]
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        transcriptTsv: {description: "A tsv file describing transcripts.", category: "required"}
+        germlineVcf: {description: "The germline VCF file from hmftools' purple.", category: "required"}
+        germlineVcfIndex: {description: "The germline VCF's index.", category: "required"}
+        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        normalName: {description: "The name of the normal sample", category: "required"}
+        outputDir: {description: "The directory the ouput should be written to.", category: "required"}
+        panelJson: {description: "A JSON describing the panel.", category: "required"}
+
+        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+        memory: {description: "The amount of memory available to the job.", 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