Nextflow Registry | nf-core/msisensor2/msi@0.0.0-0c7146d

nf-core/msisensor2/msi @ 0.0.0-0c7146d

msisensor2 detection of MSI regions.

msi microsatellite microsatellite instability tumor cfDNA

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @adamrtalbot

Maintainers: @adamrtalbot

msisensor2 detection of MSI regions.

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

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

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:57:41 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmsisensor2%2Fmsi/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/msisensor2/msi/blobs/sha256:ea11cd1cc0e9dfc8e064d834a691511ee231448ad4e9ff10df038bcfd11afedf
Size	2.8 KB
Checksum	sha256:ea11cd1cc0e9dfc8e064d834a691511ee231448ad4e9ff10df038bcfd11afedf
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:57:41 (UTC)		1	2.8 KB	-