name: mosdepth description: Calculates genome-wide sequencing coverage. keywords: - mosdepth - bam - cram - coverage tools: - mosdepth: description: | Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Input BAM/CRAM file pattern: "*.{bam,cram}" - bai: type: file description: Index for BAM/CRAM file pattern: "*.{bai,crai}" - bed: type: file description: BED file with intersected intervals pattern: "*.{bed}" - window_size: type: integer description: Window size pattern: "[0-9]+" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - global_txt: type: file description: Text file with global cumulative coverage distribution pattern: "*.{global.dist.txt}" - regions_txt: type: file description: Text file with region cumulative coverage distribution pattern: "*.{region.dist.txt}" - summary_txt: type: file description: Text file with summary mean depths per chromosome and regions pattern: "*.{summary.txt}" - per_base_bed: type: file description: BED file with per-base coverage pattern: "*.{per-base.bed.gz}" - per_base_csi: type: file description: Index file for BED file with per-base coverage pattern: "*.{per-base.bed.gz.csi}" - regions_bed: type: file description: BED file with per-region coverage pattern: "*.{regions.bed.gz}" - regions_csi: type: file description: Index file for BED file with per-region coverage pattern: "*.{regions.bed.gz.csi}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" - "@ramprasadn"