name: adapterremoval description: Trim sequencing adapters and collapse overlapping reads keywords: - trimming - adapters - merging - fastq tools: - adapterremoval: description: The AdapterRemoval v2 tool for merging and clipping reads. homepage: https://github.com/MikkelSchubert/adapterremoval documentation: https://adapterremoval.readthedocs.io licence: ["GPL v3"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false, collapse:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. pattern: "*.{fq,fastq,fg.gz,fastq.gz}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input adapter trimmed FastQ files of size 1 or 2 for single-end or collapsed data and paired-end data, respectively. pattern: "*.{fastq.gz}" - log: type: file description: AdapterRemoval log file pattern: "*.log" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@maxibor"