Nextflow Registry | nf-core/muse/sump@0.0.0-6c4ed3a

nf-core/muse/sump @ 0.0.0-6c4ed3a

Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants

variant calling somatic wgs wxs vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @famosab

Maintainers: @famosab

Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants

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

include { MUSE_SUMP } from 'nf-core/muse/sump'

MIT License

Process

`Name`	`MUSE_SUMP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`muse_call_txt` file	single input file generated by 'MuSE call' `*.MuSE.txt`
`ref_vcf` file	dbSNP vcf file that should be bgzip compressed, tabix indexed and based on the same reference genome used in 'MuSE call' `.vcf.gz`
`ref_vcf_tbi` file	Tabix index for the dbSNP vcf file `.vcf.gz.tbi`

Output 4 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.vcf.gz.tbi` map	tabix index of bgzipped vcf file with called variants `*.vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.vcf.gz` map	bgzipped vcf file with called variants `*.vcf.gz`

#3 versions_muse tuple

`${task.process}` string	The process the versions were collected from
`muse` string	The tool name
`MuSE --version \| sed -e 's/MuSE, version //g' \| sed -e 's/MuSE v//g'` string	The command used to generate the version of the tool

#4 versions_bgzip tuple

`${task.process}` string	The process the versions were collected from
`bgzip` string	The tool name
`bgzip --version \| sed -n 's/bgzip (htslib) $[0-9.]*$/\1/p'` string	The command used to generate the version of the tool

Tool	Description	Homepage
MuSE	Somatic point mutation caller based on Markov substitution model for molecular evolution	https://bioinformatics.mdanderson.org/public-software/muse/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:32:39 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fmuse%2Fsump/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/muse/sump/blobs/sha256:7d7b13d56025ddbc5b668588624ab2e0bedc37d3c65d65136823aa6f621fc7af
Size	3.2 KB
Checksum	sha256:7d7b13d56025ddbc5b668588624ab2e0bedc37d3c65d65136823aa6f621fc7af
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:32:39 (UTC)		4	3.2 KB
0.0.0-0c7146d	08 Apr 2026 19:20:36 (UTC)		2	3.2 KB