name: bedtools_slop
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
keywords:
  - bed
  - slopBed
tools:
  - bedtools:
      description: |
        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html

params:
  - l:
      type: integer
      description: The number of base pairs to subtract from the start coordinate
  - r:
      type: integer
      description: The number of base pairs to add to the end coordinate
  - b:
      type: integer
      description: Increases the entry by the same number base pairs in each direction
  - pct:
      type: boolean
      description: |
        Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.

  - header:
      type: boolean
      description: |
        Print the header from the input file prior to results.

  - 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.
  - enable_conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: List of bed files
      pattern: "*.{bed}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: Edited bed file
      pattern: "*.{slop.bed}"

  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

authors: -"@Emiller88"
  -"@sruthipsuresh"