name: "atlas_call"
description: generate VCF file from a BAM file using various calling methods
keywords:
  - atlas
  - variant calling
  - vcf
  - population genetics
tools:
  - "atlas":
      description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
      homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
      tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
      doi: "10.1101/105346"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: A BAM/ file
      pattern: "*.bam"
  - bai:
      type: file
      description: The BAI file for the input BAM file
      pattern: "*.bai"
  - fasta:
      type: file
      description: The reference FASTA file used to generate the BAM file
      pattern: "*.{fasta,fna,fa}"
  - fai:
      type: file
      description: The index of the FASTA file used for to generate the BAM file
      pattern: "*.fai"
  - recal:
      type: file
      description: Optional recalibration file from atlas recal function in text format
      pattern: "*.txt"
  - pmd:
      type: file
      description: Optional PMD file from atlas pmd function in text format
      pattern: "*.txt"
  - known_alleles:
      type: file
      description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
      pattern: "*.{txt.tsv}"
  - method:
      type: character
      description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
      pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase"

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"
  - bam:
      type: file
      description: VCF file with variant calls
      pattern: "*.vcf.gz"

authors:
  - "@jfy133"