name: samtools_depth description: Computes the depth at each position or region. keywords: - depth - samtools - statistics - coverage tools: - samtools: description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region homepage: http://www.htslib.org documentation: http://www.htslib.org/doc/samtools-depth.html tool_dev_url: https://github.com/samtools/samtools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: sorted BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - tsv: type: file description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position pattern: "*.{tsv}" authors: - "@louperelo"