Nextflow Registry | nf-core/saltshaker/classify@0.0.0-0c7146d

nf-core/saltshaker/classify @ 0.0.0-0c7146d

mtDNA deletion and duplication classification downstream of mitosalt

saltshaker mitosalt mtDNA structural-variant calling

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:19 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsaltshaker%2Fclassify/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/saltshaker/classify/blobs/sha256:8068fb70dbab37d5d5afdea34210911ddc327b7b833be77287a72d591ea90148
Size	2.9 KB
Checksum	sha256:8068fb70dbab37d5d5afdea34210911ddc327b7b833be77287a72d591ea90148
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:19 (UTC)		1	2.9 KB	-