name: "atlas_recal"
description: gives an estimation of the sequencing bias based on known invariant sites
keywords:
  - sequencing_bias
  - ATLAS
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: "None"
      doi: "https://doi.org/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: BAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: BAI file
      pattern: "*.bai"
  - empiric:
      type: file
      description: Optional txt file from PMD estimations (atlas/pmd)
      pattern: "*.txt"
  - alleles:
      type: file
      descrition: Optional bed file with known alleles
      pattern: "*.bed"
  - invariant_sites:
      type: file
      descrition: Optional bed file with invariant site coordinates
      pattern: "*.bed"

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"
  - recal_patterns:
      type: file
      description: file containing the sequencing bias for each of the Read Group pools
      pattern: "*.txt"

authors:
  - "@ltcrod"