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"