name: bedtools_getfasta description: extract sequences in a FASTA file based on intervals defined in a feature file. keywords: - bed - fasta - getfasta 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 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: - bed: type: file description: Bed feature file pattern: "*.{bed}" - fasta: type: file description: Input fasta file pattern: "*.{fa,fasta}" output: - fasta: type: file description: Output fasta file with extracted sequences pattern: "*.{fa}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@joseespinosa" - "@drpatelh"