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"