name: "msisensor2_msi"
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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  #
  - tumor_bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - normal_bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - intervals:
      type: file
      description: BED
      pattern: "*.bed"
  - models:
      type: file
      description: Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)
      pattern: "*/*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - msi:
      type: file
      description: MSI classifications as a text file
  - distribution:
      type: file
      description: Read count distributions of MSI regions
  - somatic:
      type: file
      description: Somatic MSI regions detected.
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@adamrtalbot"