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nf-core/msisensorpro/msisomatic @ 0.0.0-0c7146d

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

micro-satellite-scan msisensor-pro msi somatic
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @FriederikeHanssen
Maintainers: @FriederikeHanssen

Summary

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

Get started

Add the following snippet to your workflow script to include this module.

include { MSISENSORPRO_MSISOMATIC } from 'nf-core/msisensorpro/msisomatic'

License

MIT License

Process
Name MSISENSORPRO_MSISOMATIC
Input 3 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
normal file

BAM/CRAM/SAM file

 *.{bam,cram,sam}
normal_index file

BAM/CRAM/SAM index file

 *.{bai,crai,sai}
tumor file

BAM/CRAM/SAM file

 *.{bam,cram,sam}
tumor_index file

BAM/CRAM/SAM index file

 *.{bai,crai,sai}
intervals file

bed file containing interval information, optional

 *.{bed}
#2 tuple
meta2 map

Groovy Map containing genome information e.g. [ id:'genome' ]
fasta file

Reference genome

 *.{fasta}
msisensor_scan file

Output from msisensor-pro/scan, containing list of msi regions

 *.list
Output 5 channels
#1 output_dis tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}_dis file

File containing distribution results
#2 output_report tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix} file

File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score
#3 output_somatic tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}_somatic file

File containing somatic results
#4 output_germline tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}_germline file

File containing germline results
#5 versions_msisensorpro tuple
${task.process} string

The name of the process
msisensor-pro string

The name of the tool
msisensor-pro --version 2>&1 | sed -nE 's/Version:\s*//p' eval

The expression to obtain the version of the tool
Tool Description Homepage
msisensorpro Microsatellite Instability (MSI) detection using high-throughput sequencing data. https://github.com/xjtu-omics/msisensor-pro
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:57:42 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmsisensorpro%2Fmsisomatic/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/msisensorpro/msisomatic/blobs/sha256:d60d42d3dd253c670a4406db41d5a78ef62e82cc6f779bc9522ed5c438c99c10