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"