name: khmer_normalizebymedian
description: Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible.
keywords:
  - digital normalization
  - khmer
tools:
  - khmer:
      description: khmer k-mer counting library
      homepage: https://github.com/dib-lab/khmer
      documentation: https://khmer.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/dib-lab/khmer
      doi: "https://doi.org/10.12688/f1000research.6924.1"
      licence: ["BSD License"]

input:
  - pe_reads:
      type: files
      description: Paired-end interleaved fastq files
      pattern: "*.{fq,fastq}.gz"
  - se_reads:
      type: files
      description: Single-end fastq files
      pattern: "*.{fq,fastq}.gz"
  - name:
      type: string
      description: filename for output file(s); ".fastq.gz" will be appended

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - reads:
      type: file
      description: Interleaved fastq files
      pattern: "*.{fq,fastq}.gz"

authors:
  - "@erikrikarddaniel"