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

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

homoploymer microsatellite MSI instability
Latest version: 0.0.0-6c4ed3a
Total downloads: 3
Source: nf-core/modules
Authors: @kevbrick
Maintainers: @kevbrick

Summary

Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data

Get started

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

include { MSISENSOR_MSI } from 'nf-core/msisensor/msi'

License

MIT License

Process
Name MSISENSOR_MSI
Input 1 channel
#1 tuple
meta map

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

Coordinate sorted BAM/CRAM/SAM file from normal tissue

 *.{bam,cram,sam}
normal_bai file

Index for coordinate sorted BAM/CRAM/SAM file from normal tissue

 *.{bam,cram,sam}
tumor_bam file

Coordinate sorted BAM/CRAM/SAM file from tumor tissue

 *.{bam,cram,sam}
tumor_bai file

Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue

 *.{bam,cram,sam}
metascan file

metascan file
homopolymers file

Output file from MSIsensor scan module

 *.msisensor_scan.tab
Output 5 channels
#1 output tuple
meta map

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

Output file from MSIsensor msi module
#2 versions
versions.yml file

File containing software versions

 versions.yml
#3 output_dis tuple
meta map

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

Output file from MSIsensor module
#4 output_somatic tuple
meta map

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

Output file from MSIsensor module
#5 output_germline tuple
meta map

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

Output file from MSIsensor module
Tool Description Homepage
msisensor MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. https://github.com/ding-lab/msisensor
Version 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:23:00 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fmsisensor%2Fmsi/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/msisensor/msi/blobs/sha256:6f2b0d76ae996464f5b70d169487a26cfe2f7102e40b86f90ab58679eeb63968
Size 3.0 KB
Checksum sha256:6f2b0d76ae996464f5b70d169487a26cfe2f7102e40b86f90ab58679eeb63968
Downloads 1
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:32:17 (UTC) 1 2.9 KB
0.0.0-3fc6d40 22 Apr 2026 15:23:00 (UTC) 1 3.0 KB
0.0.0-0c7146d