name: adapterremovalfixprefix
description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
keywords:
  - adapterremoval
  - fastq
  - dedup
tools:
  - adapterremovalfixprefix:
      description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
      homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
      documentation: None
      tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
      doi: "10.1186/s13059-016-0918-z"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description: FASTQ file from AdapterRemoval2
      pattern: "*.{fq.gz,fastq.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fixed_fastq:
      type: file
      description: FASTQ file with fixed read prefixes for DeDup
      pattern: "*.{fq.gz}"

authors:
  - "@jfy133"