name: gatk4_splitncigarreads description: Splits reads that contain Ns in their cigar string keywords: - vcf - merge tools: - gatk4: description: | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 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'] - bam: type: list description: BAM/SAM/CRAM file containing reads pattern: "*.{bam,sam,cram}" - fasta: type: tuple of files description: | Tuple of fasta file (first), sequence dict (second) and fasta index (third) pattern: ["*.fasta", "*.dict", "*.fai"] output: - bam: type: file description: Output file with split reads (BAM/SAM/CRAM) pattern: "*.{bam,sam,cram}" - version: type: file description: File containing software version pattern: "*.version.txt" authors: - "@kevinmenden"