name: pydamage_analyze description: Damage parameter estimation for ancient DNA keywords: - ancient DNA - aDNA - de novo assembly - filtering - damage - deamination - miscoding lesions - C to T - palaeogenomics - archaeogenomics - palaeogenetics - archaeogenetics tools: - pydamage: description: Damage parameter estimation for ancient DNA homepage: https://github.com/maxibor/pydamage documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage 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}" - bai: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - csv: type: file description: PyDamage results as csv files pattern: "*.csv" authors: - "@maxibor"