name: hmmcopy_readcounter description: readCounter function from HMMcopy utilities, used to generate read in windows keywords: - hmmcopy - readcounter - cnv tools: - hmmcopy: description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils doi: "" 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/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" - wig: type: file description: A wig file with the number of reads lying within each window in each chromosome pattern: "*.wig" authors: - "@sppearce"