name: msisensor_msi

description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
keywords:
  - homoploymer,microsatellite
tools:
  - msisensor:
      description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
      homepage: https://github.com/ding-lab/msisensor
      documentation: None
      tool_dev_url: None
      doi: "10.1093/bioinformatics/btt755"
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - normal_bam:
      type: file
      description: Coordinate sorted BAM/CRAM/SAM file from normal tissue
      pattern: "*.{bam,cram,sam}"
  - normal_bai:
      type: file
      description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue
      pattern: "*.{bam,cram,sam}"
  - tumor_bam:
      type: file
      description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue
      pattern: "*.{bam,cram,sam}"
  - tumor_bai:
      type: file
      description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue
      pattern: "*.{bam,cram,sam}"
  - homopolymers:
      type: file
      description: Output file from MSIsensor scan module
      pattern: "*.msisensor_scan.tab"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - txt:
      type: file
      description: MSIsensor MSI final report file
      pattern: "*.output"
  - txt:
      type: file
      description: MSIsensor MSI DIS report file
      pattern: "*.output_dis"
  - txt:
      type: file
      description: MSIsensor MSI germline report file
      pattern: "*.output_germline"
  - txt:
      type: file
      description: MSIsensor MSI somatic report file
      pattern: "*.output_somatic"
authors:
  - "@kevbrick"