name: bedtools_intersect
description: Allows one to screen for overlaps between two sets of genomic features.
keywords:
  - bed
  - intersect
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/intersect.html
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - intervals1:
      type: file
      description: BAM/BED/GFF/VCF
      pattern: "*.{bam|bed|gff|vcf}"
  - intervals2:
      type: file
      description: BAM/BED/GFF/VCF
      pattern: "*.{bam|bed|gff|vcf}"
  - extension:
      type: value
      description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - intersect:
      type: file
      description: File containing the description of overlaps found between the two features
      pattern: "*.${extension}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@Emiller88"
  - "@sruthipsuresh"
  - "@drpatelh"
  - "@sidorov-si"
