name: gatk4_estimatelibrarycomplexity description: Estimates the numbers of unique molecules in a sequencing library. keywords: - gatk4 - gatk4_estimatelibrarycomplexity - duplication_metrics - reporting tools: - gatk4: description: Genome Analysis Toolkit (GATK4) homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us tool_dev_url: https://github.com/broadinstitute/gatk 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', single_end:false ] - cram: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fai: type: file description: Index of reference fasta file pattern: "fasta.fai" - dict: type: file description: GATK sequence dictionary pattern: "*.dict" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - metrics: type: file description: File containing metrics on the input files pattern: "*.{metrics}" authors: - "@FriederikeHanssen"