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 ] - versions: type: file description: File containing software versions pattern: "versions.yml" - 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"