name: sentieon_dnamodelapply
description: modifies the input VCF file by adding the MLrejected FILTER to the variants
keywords:
  - dnamodelapply
  - vcf
  - filter
  - 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' ]`
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. `[ id:'test' ]`
  - vcf:
      type: file
      description: INPUT VCF file
      pattern: "*.{vcf,vcf.gz}"
  - idx:
      type: file
      description: Index of the input VCF file
      pattern: "*.{tbi}"
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: Index of the genome fasta file
      pattern: "*.fai"
  - ml_model:
      type: file
      description: machine learning model file
      pattern: "*.model"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - vcf:
      type: file
      description: INPUT VCF file
      pattern: "*.{vcf,vcf.gz}"
  - index:
      type: file
      description: Index of the input VCF file
      pattern: "*.{tbi}"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
