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
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}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@Emiller88"
    - "@sruthipsuresh"
    - "@drpatelh"
    - "@sidorov-si"