Nextflow Registry | nf-core/muse/sump@0.0.0-0c7146d

nf-core/muse/sump @ 0.0.0-0c7146d

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: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:58:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmuse%2Fsump/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/muse/sump/blobs/sha256:2006de7c3d1dcdfb1c58cf350a2055b7e64c64aeecde5a30d95f5adb3a1a29e8
Size	3.2 KB
Checksum	sha256:2006de7c3d1dcdfb1c58cf350a2055b7e64c64aeecde5a30d95f5adb3a1a29e8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:58:10 (UTC)		1	3.2 KB	-