nf-core_modules/software/msisensor/msi/meta.yml

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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"