name: tiddit_cov description: Computes the coverage of different regions from the bam file. keywords: - coverage - bam - statistics - chromosomal rearrangements tools: - tiddit: description: TIDDIT - structural variant calling. homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: "10.12688/f1000research.11168.1" licence: ["GPL v3"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" - fasta: type: file description: | Reference genome file. Only needed when passing in CRAM instead of BAM. If not using CRAM, please pass an empty file instead. pattern: "*.fasta" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - cov: type: file description: The coverage of different regions. Optional. pattern: "*.tab" - wig: type: file description: The coverage of different regions in WIG format. Optional. pattern: "*.wig" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@projectoriented"