name: deeptools_bamcoverage description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. keywords: - sort tools: - deeptools: description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html tool_dev_url: https://github.com/deeptools/deepTools/ doi: "https://doi.org/10.1093/nar/gkw257" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" - input_index: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" 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" - bigWig: type: file description: BigWig file pattern: "*.bigWig" - bedgraph: type: file description: Bedgraph file pattern: "*.bedgraph" authors: - "@FriederikeHanssen"