name: sentieon_dnascope
description: DNAscope algorithm performs an improved version of Haplotype variant calling.
keywords:
  - dnascope
  - sentieon
  - variant_calling
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 ]
  - bam:
      type: file
      description: BAM file.
      pattern: "*.bam"
  - bai:
      type: file
      description: BAI file
      pattern: "*.bai"
  - intervals:
      type: file
      description: bed or interval_list file containing interval in the reference that will be used in the analysis
      pattern: "*.{bed,interval_list}"
  - meta2:
      type: map
      description: |
        Groovy Map containing meta information for fasta.
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta}"
  - meta3:
      type: map
      description: |
        Groovy Map containing meta information for fasta index.
  - fai:
      type: file
      description: Index of the genome fasta file
      pattern: "*.fai"
  - meta4:
      type: map
      description: |
        Groovy Map containing meta information for dbsnp.
  - dbsnp:
      type: file
      description: Single Nucleotide Polymorphism database (dbSNP) file
      pattern: "*.vcf.gz"
  - meta5:
      type: map
      description: |
        Groovy Map containing meta information for dbsnp_tbi.
  - dbsnp_tbi:
      type: file
      description: Index of the Single Nucleotide Polymorphism database (dbSNP) file
      pattern: "*.vcf.gz.tbi"
  - meta6:
      type: map
      description: |
        Groovy Map containing meta information for machine learning model for Dnascope.
  - ml_model:
      type: file
      description: machine learning model file
      pattern: "*.model"
  - ml_model:
      type: file
      description: machine learning model file
      pattern: "*.model"
  - pcr_indel_model:
      type: string
      description: |
        Controls the option pcr_indel_model for Dnascope.
        The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE".
        See Sentieons documentation for further explanation.
  - emit_vcf:
      type: string
      description: |
        Controls the vcf output from Dnascope.
        Possible options are "all", "confident" and "variant".
        See Sentieons documentation for further explanation.
  - 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:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
