nf-core_modules/software/trimgalore/meta.yml

name: trimgalore
description: Trim FastQ files using Trim Galore!
keywords:
  - trimming
  - adapters
  - sequencing adapters
tools:
  - trimgalore:
      description: |
        A wrapper tool around Cutadapt and FastQC to consistently apply quality
        and adapter trimming to FastQ files, with some extra functionality for
        MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
      homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
      documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
params:
  - outdir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$params.outdir/<SOFTWARE>`
  - publish_dir_mode:
      type: string
      description: |
        Value for the Nextflow `publishDir` mode parameter.
        Available: symlink, rellink, link, copy, copyNoFollow, move.
  - conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive
  - clip_r1:
      type: integer
      description: |
        Instructs Trim Galore to remove bp from the 5' end of read 1
        (or single-end reads)
  - clip_r2:
      type: integer
      description: |
        Instructs Trim Galore to remove bp from the 5' end of read 2
        (paired-end reads only)
  - three_prime_clip_r1:
      type: integer
      description: |
        Instructs Trim Galore to remove bp from the 3' end of read 1
        AFTER adapter/quality trimming has been performed
  - three_prime_clip_r2:
      type: integer
      description: |
        Instructs Trim Galore to re move bp from the 3' end of read 2
        AFTER adapter/quality trimming has been performed
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.
  - options:
      type: map
      description: |
        Groovy Map containing module options for passing command-line arguments and
        output file paths.
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 and 2 for
        single-end and paired-end data, respectively.
      pattern: "*.fq.gz"
  - html:
      type: file
      description: FastQC report (optional)
      pattern: "*_fastqc.html"
  - zip:
      type: file
      description: FastQC report archive (optional)
      pattern: "*_fastqc.zip"
  - log:
      type: file
      description: Trim Galore! trimming report
      pattern: "*report.txt"
  - version:
      type: file
      description: File containing software version
      pattern: "*.version.txt"
authors:
    - "@drpatelh"
    - "@ewels"
    - "@FelixKrueger"