name: sentieon_haplotyper
description: Runs Sentieon's haplotyper for germline variant calling.
keywords:
  - sentieon
  - haplotypecaller
  - haplotype
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 reference 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}"
  - intervals:
      type: file
      description: Bed file with the genomic regions included in the library (optional)
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: The index of the FASTA reference.
      pattern: "*.fai"
  - dbsnp:
      type: file
      description: VCF file containing known sites (optional)
  - dbsnp_tbi:
      type: file
      description: VCF index of dbsnp (optional)
  - emit_vcf:
      type: string
      description: |
        Controls the vcf output from the haplotyper.
        If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all".
        If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident".
        If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident".
  - emit_gvcf:
      type: boolean
      description: If true, the haplotyper will output a gvcf
output:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information.
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.unfiltered.vcf.gz"
  - vcf_tbi:
      type: file
      description: Index of VCF file
      pattern: "*.unfiltered.vcf.gz.tbi"
  - gvcf:
      type: file
      description: Compressed GVCF file
      pattern: "*.g.vcf.gz"
  - gvcf_tbi:
      type: file
      description: Index of GVCF file
      pattern: "*.g.vcf.gz.tbi"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@asp8200"
