name: bedtools_complement description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. keywords: - bed - complement 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/complement.html params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/` - 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 - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: Input BED file pattern: "*.{bed}" - sizes: type: file description: File which defines the chromosome lengths for a given genome pattern: "*.{sizes}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: Bed file with all genomic intervals that are not covered by at least one record from the input file. pattern: "*.{bed}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@Emiller88" - "@sruthipsuresh" - "@drpatelh"