name: "crisprcleanr_normalize"
description: remove false positives of functional crispr genomics due to CNVs
keywords:
  - sort
  - CNV
  - correction
  - CRISPR
tools:
  - "crisprcleanr":
      description: "Analysis of CRISPR functional genomics, remove false positive due to CNVs."
      homepage: "https://github.com/francescojm/CRISPRcleanR"
      documentation: "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf"
      tool_dev_url: "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0"
      doi: "10.1186/s12864-018-4989-y"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - count_file:
      type: file
      description: sgRNA raw counts
      pattern: "*.tsv"
  - library_file:
      type: file
      description: sgRNA library
      pattern: "*.tsv"

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"
  - norm_count_file:
      type: file
      description: normalized count file
      pattern: "*.tsv"

authors:
  - "@LaurenceKuhl"
