Nextflow Registry | nf-core/saltshaker/classify@0.0.0-6c4ed3a

nf-core/saltshaker/classify @ 0.0.0-6c4ed3a

mtDNA deletion and duplication classification downstream of mitosalt

saltshaker mitosalt mtDNA structural-variant calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @ieduba

Maintainers: @ieduba

mtDNA deletion and duplication classification downstream of mitosalt

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

include { SALTSHAKER_CLASSIFY } from 'nf-core/saltshaker/classify'

MIT License

Process

`Name`	`SALTSHAKER_CLASSIFY`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`call` file	call metadata file from saltshaker_call `*_call_metadata.tsv`

`mito_name` string	Name of the mitochondrial chromosome

Output 4 channels

#1 txt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_classify.txt` file	txt file with case classification `*_classify.txt`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*saltshaker.vcf` file	vcf file with classified calls `*saltshaker.vcf`

#3 classify tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_classify_metadata.tsv` file	tsv with classified call metadata to be used in saltshaker_plot `*_classify_metadata.tsv`

#4 versions_saltshaker tuple

`${task.process}` string	The name of the process
`saltshaker` string	The name of the tool
`1.0.1` string	Hardcoded version of saltshaker used in the module

Tool	Description	Homepage
saltshaker	A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output.	https://github.com/aksenia/saltshaker

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:41:49 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsaltshaker%2Fclassify/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/saltshaker/classify/blobs/sha256:15c3634f77df3f3b7cdacaf0ae03b8e50cce13b391641914f76f44d43712072a
Size	2.9 KB
Checksum	sha256:15c3634f77df3f3b7cdacaf0ae03b8e50cce13b391641914f76f44d43712072a
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:41:49 (UTC)		4	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:32:57 (UTC)		3	2.9 KB