name: gatk4_estimatelibrarycomplexity
description: Estimates the numbers of unique molecules in a sequencing library.
keywords:
  - duplication metrics
  - estimatelibrarycomplexity
  - gatk4
  - 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"]
      identifier: ""
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:
  - metrics:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.metrics":
          type: file
          description: File containing metrics on the input files
          pattern: "*.{metrics}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@FriederikeHanssen"
  - "@maxulysse"
maintainers:
  - "@FriederikeHanssen"
  - "@maxulysse"
