name: "kmcp_search"
description: Search sequences against database
keywords:
  - metagenomics
  - classify
  - taxonomic profiling
  - fastq
  - sequences
  - kmers
tools:
  - "kmcp":
      description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping"
      homepage: "https://github.com/shenwei356/kmcp"
      documentation: "https://github.com/shenwei356/kmcp#documents"
      tool_dev_url: "https://github.com/shenwei356/kmcp"
      doi: "10.1093/bioinformatics/btac845"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - db:
      type: directory
      description: Database directory created by "kmcp index"
      pattern: "*"
  - reads:
      type: file
      description: gzipped fasta or fastq files
      pattern: "*.{fq.gz,fastq.gz,fa.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - result:
      type: file
      description: Output file in tab-delimited format with 15 columns
      pattern: "*.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sofstam"
