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nf-core/msisensor2/msi @ 0.0.0-3fc6d40

msisensor2 detection of MSI regions.

msi microsatellite microsatellite instability tumor cfDNA
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @adamrtalbot
Maintainers: @adamrtalbot

Summary

msisensor2 detection of MSI regions.

Get started

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

include { MSISENSOR2_MSI } from 'nf-core/msisensor2/msi'

License

MIT License

Process
Name MSISENSOR2_MSI
Input 2 channels
#1 tuple
meta map

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

BAM/CRAM/SAM file

 *.{bam,cram,sam}
tumor_bam_index file

BAM/CRAM/SAM index file

 *.{bai,crai}
#2 tuple
meta2 map

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

Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)

 */*
Output 4 channels
#1 msi tuple
meta map

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

MSI classifications as a text file
#2 somatic tuple
meta map

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

Somatic MSI regions detected.
#3 distribution tuple
meta map

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

Read count distributions of MSI regions
#4 versions_msisensor2 tuple
${task.process} string

The name of the process
msisensor2 string

The name of the tool
msisensor2 2> >(grep Version) | sed 's/Version: v//g' eval

The expression to obtain the version of the tool
Tool Description Homepage
msisensor2 MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data. https://github.com/niu-lab/msisensor2
Version 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:23:03 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fmsisensor2%2Fmsi/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/msisensor2/msi/blobs/sha256:9ff6957bff3d5f8ad1cfe312b5c5bf024cf1ddae3fb8c23e94e9a4e8957e67ae
Size 2.8 KB
Checksum sha256:9ff6957bff3d5f8ad1cfe312b5c5bf024cf1ddae3fb8c23e94e9a4e8957e67ae
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:32:19 (UTC) 3 2.8 KB
0.0.0-3fc6d40 22 Apr 2026 15:23:03 (UTC) 3 2.8 KB
0.0.0-0c7146d 08 Apr 2026 19:20:07 (UTC) 3 2.8 KB