name: gatk4_learnreadorientationmodel description: | Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts keywords: - gatk4 - learnreadorientationmodel - readorientationartifacts - mutect2 tools: - gatk4: description: | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ['Apache-2.0'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - f1r2: type: list description: list of f1r2 files to be used as input. pattern: "*.f1r2.tar.gz" output: - artifactprior: type: file description: file containing artifact-priors to be used by filtermutectcalls pattern: "*.tar.gz" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"