Nextflow Registry | nf-core/msisensorpro/pro@0.0.0-6c4ed3a

nf-core/msisensorpro/pro @ 0.0.0-6c4ed3a

MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample sequencing data

msisensor-pro pro micro-satellite

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @Tuur-ds

Maintainers: @Tuur-ds

MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample sequencing data

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

include { MSISENSORPRO_PRO } from 'nf-core/msisensorpro/pro'

MIT License

Process

`Name`	`MSISENSORPRO_PRO`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`input` file	sorted BAM/CRAM file `*.{bam,cram}`
`index` file	index file for input `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`list` file	micro-satellite list `*.{list}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	reference genome used to create micro-satellite list `*.{fasta}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fai` file	index file for reference fasta `*.{fai}`

Output 5 channels

#1 all_msi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_all` file	txt file containing all results

#2 dis_msi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_dis` file	txt file containing the allele length distribution

#3 summary_msi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}` file	txt file containing summary of results

#4 unstable_msi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_unstable` file	txt file containing unstable micro-satellite sites

#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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:32:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fmsisensorpro%2Fpro/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/msisensorpro/pro/blobs/sha256:d25520a31fd27d95bb0f719f27ef51b2e5b26e5612061e8836147f7ec195c96b
Size	2.9 KB