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 ]
  - input:
      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"
  - "@maxulysse"