name: gatk4_createsomaticpanelofnormals description: Create a panel of normals contraining germline and artifactual sites for use with mutect2. keywords: - gatk4 - createsomaticpanelofnormals - panelofnormals 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 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test'] - genoomicsdb: type: directory description: genomicsDB workspace that contains the samples to create the somatic panel of normals with. pattern: "*_genomicsDBworkspace" - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fastaidx: type: file description: Index of reference fasta file pattern: "fasta.fai" - dict: type: file description: GATK sequence dictionary pattern: "*.dict" output: - vcf: type: file description: panel of normal as compressed vcf file pattern: "*.vcf.gz" - tbi: type: file description: Index of vcf file pattern: "*vcf.gz.tbi" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"