name: "prinseqplusplus"
description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
keywords:
  - fastq
  - fasta
  - filter
  - trim
tools:
  - "prinseqplusplus":
      description: "PRINSEQ++ - Multi-threaded C++ sequence cleaning"
      homepage: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
      documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
      tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
      doi: "10.7287/peerj.preprints.27553v1"
      licence: "['GPL v2']"

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.

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"
  - good_reads:
      type: file
      description: Reads passing filter(s) in gzipped FASTQ format
      pattern: "*_good_out_{R1,R2}.fastq.gz"
  - single_reads:
      type: file
      description: |
        Single reads without the pair passing filter(s) in gzipped FASTQ format
      pattern: "*_single_out_{R1,R2}.fastq.gz"
  - bad_reads:
      type: file
      description: |
        Reads without not passing filter(s) in gzipped FASTQ format
      pattern: "*_bad_out_{R1,R2}.fastq.gz"
  - log:
      type: file
      description: |
        Verbose level 2 STDOUT information in a log file
      pattern: "*.log"

authors:
  - "@jfy133"