diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c3a3744b744383e7e3bbc4fc526e8223ef6efb5..797ca07bfe6284a41ee78f658844b6ed0de36185 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/smoove.wdl b/smoove.wdl new file mode 100644 index 0000000000000000000000000000000000000000..e8846f72b48ea5e0702af49c0954e6d27e20812c --- /dev/null +++ b/smoove.wdl @@ -0,0 +1,72 @@ +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"} + } +}