diff --git a/extractSigPredictHRD.wdl b/extractSigPredictHRD.wdl new file mode 100644 index 0000000000000000000000000000000000000000..6aa5ff1d49a8a1288f1412474b6097415064af1c --- /dev/null +++ b/extractSigPredictHRD.wdl @@ -0,0 +1,69 @@ +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 ExtractSigPredictHRD { + input { + String outputDir = "." + String sampleName + File snvIndelVcf + File snvIndelVcfIndex + File svVcf + File svVcfIndex + + String memory = "8G" + Int timeMinutes = 15 + String dockerImage = "quay.io/biowdl/chord-mutsigextractor:2.00_1.14" + } + + command { + extractSigPredictHRD.R \ + ~{outputDir} \ + ~{sampleName} \ + ~{snvIndelVcf} \ + ~{svVcf} \ + } + + output { + File chordPrediction = "~{outputDir}/~{sampleName}_chord_prediction.txt" + File chordSignatures = "~{outputDir}/~{sampleName}_chord_signatures.txt" + } + + runtime { + memory: memory + time_minutes: timeMinutes # !UnknownRuntimeKey + docker: dockerImage + } + + parameter_meta { + outputDir: {description: "The directory the outout will be written to.", category: "required"} + sampleName: {description: "The name of the sample.", category: "required"} + snvIndelVcf: {description: "A VCF file with SNVs and indels.", category: "required"} + snvIndelVcfIndex: {description: "The index for the SNV/indel VCF file.", category: "required"} + svVcf: {description: "A VCF file with SVs.", category: "required"} + svVcfIndex: {description: "The index for the SV VCF file.", category: "required"} + + memory: {description: "The amount of memory this job will use.", category: "advanced"} + timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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