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"