name: cmseq_polymut description: Calculates polymorphic site rates over protein coding genes keywords: - polymut - polymorphic - mags - assembly - polymorphic sites - estimation - protein coding genes - cmseq - bam - coverage tools: - cmseq: description: Set of utilities on sequences and BAM files homepage: https://github.com/SegataLab/cmseq documentation: https://github.com/SegataLab/cmseq tool_dev_url: https://github.com/SegataLab/cmseq licence: ['MIT License'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.bam" - bai: type: file description: BAM index file pattern: "*.bai" - gff: type: file description: GFF file used to extract protein-coding genes pattern: "*.gff" - fasta: type: file description: Optional fasta file to run on a subset of references in the BAM file. pattern: .{fa,fasta,fas,fna} 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" - polymut: type: file description: Polymut report in `.txt` format. pattern: "*.txt" authors: - "@maxibor"