name: damageprofiler
description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
keywords:
  - damage
  - deamination
  - miscoding lesions
  - C to T
  - ancient DNA
  - aDNA
  - palaeogenomics
  - archaeogenomics
  - palaeogenetics
  - archaeogenetics
tools:
  - damageprofiler:
      description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
      homepage: https://github.com/Integrative-Transcriptomics/DamageProfiler
      documentation: https://damageprofiler.readthedocs.io/
      tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler
      doi: "10.1093/bioinformatics/btab190"
      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/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - fasta:
      type: file
      description: OPTIONAL FASTA reference file
      pattern: "*.{fasta,fna,fa}"
  - fai:
      type: file
      description: OPTIONAL FASTA index file from samtools faidx
      pattern: "*.{fai}"
  - specieslist:
      type: file
      description: OPTIONAL text file with list of target reference headers
      pattern: "*.{txt}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - results:
      type: dir
      description: DamageProfiler results directory
      pattern: "*/*"

authors:
  - "@jfy133"