name: msisensorpro_msi_somatic
description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input
keywords:
  - micro-satellite-scan
  - msisensor-pro
  - msi
  - somatic
tools:
  - msisensorpro:
      description: Microsatellite Instability (MSI) detection using high-throughput sequencing data.
      homepage: https://github.com/xjtu-omics/msisensor-pro
      documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
      tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
      doi: "10.1016/j.gpb.2020.02.001"
      licence: ["Custom Licence"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - normal:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - normal_index:
      type: file
      description: BAM/CRAM/SAM index file
      pattern: "*.{bai,crai,sai}"
  - tumor:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - tumor_index:
      type: file
      description: BAM/CRAM/SAM index file
      pattern: "*.{bai,crai,sai}"
  - intervals:
      type: file
      description: bed file containing interval information, optional
      pattern: "*.{bed}"
  - fasta:
      type: file
      description: Reference genome
      pattern: "*.{fasta}"
  - msisensor_scan:
      type: file
      description: Output from msisensor-pro/scan, conaining list of msi regions
      pattern: "*.list"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - output_report:
      type: file
      description: File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score
  - output_dis:
      type: file
      description: File containing distribution results
  - output_germline:
      type: file
      description: File containing germline results
  - output_somatic:
      type: file
      description: File containing somatic results
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - list:
      type: file
      description: File containing microsatellite list
      pattern: "*.{list}"

authors:
  - "@FriederikeHanssen"
