name: gatk4_applybqsr
description: Apply base quality score recalibration (BQSR) to a bam file
keywords:
  - bqsr
  - bam
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', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM file from alignment
      pattern: "*.{bam,cram}"
  - input_index:
      type: file
      description: BAI/CRAI file from alignment
      pattern: "*.{bai,crai}"
  - bqsr_table:
      type: file
      description: Recalibration table from gatk4_baserecalibrator
  - intervals:
      type: file
      description: Bed file with the genomic regions included in the library (optional)
  - 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"
  - bam:
      type: file
      description: Recalibrated BAM file
      pattern: "*.{bam}"
  - cram:
      type: file
      description: Recalibrated CRAM file
      pattern: "*.{cram}"

authors:
  - "@yocra3"
  - "@FriederikeHanssen"
