name: sentieon_varcal
description: |
  Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR).
  VarCal builds a recalibration model for scoring variant quality.
  https://support.sentieon.com/manual/usages/general/#varcal-algorithm
keywords:
  - sentieon
  - varcal
  - variant recalibration
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' ]
  - vcf:
      type: file
      description: input vcf file containing the variants to be recalibrated
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: tbi file matching with -vcf
      pattern: "*.vcf.gz.tbi"
  - resource_vcf:
      type: file
      description: all resource vcf files that are used with the corresponding '--resource' label
      pattern: "*.vcf.gz"
  - resource_tbi:
      type: file
      description: all resource tbi files that are used with the corresponding '--resource' label
      pattern: "*.vcf.gz.tbi"
  - labels:
      type: string
      description: necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: Index of reference fasta file
      pattern: "fasta.fai"
output:
  - recal:
      type: file
      description: Output recal file used by ApplyVQSR
      pattern: "*.recal"
  - idx:
      type: file
      description: Index file for the recal output file
      pattern: "*.idx"
  - tranches:
      type: file
      description: Output tranches file used by ApplyVQSR
      pattern: "*.tranches"
  - plots:
      type: file
      description: Optional output rscript file to aid in visualization of the input data and learned model.
      pattern: "*plots.R"
  - version:
      type: file
      description: File containing software versions
      pattern: "*.versions.yml"
authors:
  - "@asp8200"
maintainers:
  - "@asp8200"
