name: "msisensor2_scan"
description: msisensor2 detection of MSI regions.
keywords:
  - msi
tools:
  - "msisensor2":
      description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data."
      homepage: "https://github.com/niu-lab/msisensor2"
      documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md"
      tool_dev_url: "https://github.com/niu-lab/msisensor2"
      doi: ""
      licence: "GPL-3.0"

input:
  - fasta:
      type: file
      description: Path to reference genome.
      pattern: "*.fasta"
  - output:
      type: val
      description: Name of output MSI scan to write.

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - output:
      type: file
      description: Output scan of MSI regions in FASTA file.
      pattern: "*"

authors:
  - "@adamrtalbot"