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

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

mtDNA deletion and duplication calling 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 calling downstream of mitosalt

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

include { SALTSHAKER_CALL } from 'nf-core/saltshaker/call'

MIT License

Process

`Name`	`SALTSHAKER_CALL`

Input 9 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`breakpoint` file	breakpoint file from mitosalt `*.{breakpoint}`
`cluster` file	cluster file from mitosalt `*.{cluster}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'fasta' ]
`mtfasta` file	Reference mitochondrial genome in FASTA format `*.{fasta,fa}`

`flank` integer	Basepairs flanking a deletion

`heteroplasmy_limit` float	Minimum heteroplasmy level to report a deletion/duplication

`mito_length` integer	Length of the mitochondrial genome

`heavy_strand_origin_start` integer	Start position of the heavy strand origin of replication

`heavy_strand_origin_end` integer	End position of the heavy strand origin of replication

`light_strand_origin_start` integer	Start position of the light strand origin of replication

`light_strand_origin_end` integer	End position of the light strand origin of replication

Output 2 channels

#1 call tuple

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

#2 versions_saltshaker tuple

`${task.process}` string	The name of the process
`saltshaker` string	The name of the tool
`1.0.0` 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 19:09:17 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsaltshaker%2Fcall/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/saltshaker/call/blobs/sha256:ef54589d234bab90db0e83bd0f78cd143145e7e7e0b70096e6e3cf8621728f05
Size	2.7 KB
Checksum	sha256:ef54589d234bab90db0e83bd0f78cd143145e7e7e0b70096e6e3cf8621728f05
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:17 (UTC)		1	2.7 KB	-