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 ]
  - 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,fq.gz,fastq.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - singles_truncated:
      type: file
      description: |
        Adapter trimmed FastQ files of either single-end reads, or singleton
        'orphaned' reads from merging of paired-end data (i.e., one of the pair
        was lost due to filtering thresholds).
      pattern: "*.truncated.gz"
  - discarded:
      type: file
      description: |
        Adapter trimmed FastQ files of reads that did not pass filtering
        thresholds.
      pattern: "*.discarded.gz"
  - pair1_truncated:
      type: file
      description: |
        Adapter trimmed R1 FastQ files of paired-end reads that did not merge
        with their respective R2 pair due to long templates. The respective pair
        is stored in 'pair2_truncated'.
      pattern: "*.pair1.truncated.gz"
  - pair2_truncated:
      type: file
      description: |
        Adapter trimmed R2 FastQ files of paired-end reads that did not merge
        with their respective R1 pair due to long templates. The respective pair
        is stored in 'pair1_truncated'.
      pattern: "*.pair2.truncated.gz"
  - collapsed:
      type: file
      description: |
        Collapsed FastQ of paired-end reads that successfully merged with their
        respective R1 pair but were not trimmed.
      pattern: "*.collapsed.gz"
  - collapsed_truncated:
      type: file
      description: |
        Collapsed FastQ of paired-end reads that successfully merged with their
        respective R1 pair and were trimmed of adapter due to sufficient overlap.
      pattern: "*.collapsed.truncated.gz"
  - log:
      type: file
      description: AdapterRemoval log file
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@maxibor"
  - "@jfy133"