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 licence: ["Apache-2.0"] 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: file description: The reference fasta file pattern: "*.fasta" - fai: type: file description: Index of reference fasta file pattern: "*.fasta.fai" - dict: type: file description: GATK sequence dictionary pattern: "*.dict" output: - bam: type: file description: Output file with split reads (BAM/SAM/CRAM) pattern: "*.{bam,sam,cram}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@kevinmenden"