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

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file from alignment
      pattern: "*.{bam}"
  - bqsr_table:
      type: file
      description: Recalibration table from gatk4_baserecalibrator
  - fasta:
      type: file
      description: The reference fasta file
  - fastaidx:
      type: file
      description: Index of reference fasta file
  - dict:
      type: file
      description: GATK sequence dictionary
  - intervalsBed:
      type: file
      description: Bed file with the genomic regions included in the library (optional)

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - bam:
      type: file
      description: Recalibrated BAM file
      pattern: "*.{bam}"

authors:
  - "@yocra3"