name: sentieon_readwriter
description: Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.
keywords:
  - merge
  - convert
  - readwriter
  - sentieon
tools:
  - sentieon:
      description: |
        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
      homepage: https://www.sentieon.com/
      documentation: https://www.sentieon.com/
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information.
        e.g. [ id:'test', single_end:false ]
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test' ]
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test' ]
  - input:
      type: file
      description: BAM/CRAM file.
      pattern: "*.{bam,cram}"
  - index:
      type: file
      description: BAI/CRAI file.
      pattern: "*.{bai,crai}"
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: The index of the FASTA reference.
      pattern: "*.fai"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test', single_end:false ]
  - output:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - index:
      type: file
      description: BAM/CRAM index file
      pattern: "*.{bai,crai}"
  - output_index:
      type: file
      description: BAM/CRAM alignment and the corresponding index file
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
