Nextflow Registry | nf-core/custom/geneticmapconvert@0.0.0-0c7146d

nf-core/custom/geneticmapconvert @ 0.0.0-0c7146d

This R script allows to automatically detect the different genetic map format and convert the input file in all the other format type.

map convertion R

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LouisLeNezet

Maintainers: @LouisLeNezet

Summary

This R script allows to automatically detect the different genetic map format and convert the input file in all the other format type.

Get started

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

include { CUSTOM_GENETICMAPCONVERT } from 'nf-core/custom/geneticmapconvert'

License

MIT License

Process

`Name`	`CUSTOM_GENETICMAPCONVERT`

Input 1 channel

#1 tuple

meta map

Groovy Map containing sample information e.g. [ id:'test' ]

map_file file

Genomic map file to process. This file should contain the data of only one chromosome. It should be a flat file (comma, semicolon, tab or space delimited) with at least the physical position and its corresponding recombination distance in centiMorgans. The columns names will be normalised (no space, extra character transformed to "_") and then automatically recognise as:

chr: _chr, chrom, chromosome
pos: position, bp
id: snp, marker, rsid
cm: genetic_map_cm
rate: combined_rate, combined_rate_cm_mb, cm_mb If no header present, then it will try for 3 columns table with chr, pos, cm format and for 4 columns table with chr, id, cm, pos format.

Output 5 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 plink_map tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.plink.map` file	File containing the map in PLINK format: space-delimited file without header and columns: chr, id, cM, pos `*.plink.map`

#3 stitch_map tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.stitch.map` file	File containing the map in STITCH format: space-delimited file with header and columns: pos, rate, cM `*.stitch.map`

#4 glimpse_map tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.glimpse.map` file	File containing the map in Glimpse format: tab-delimited file with header and columns: pos, chr, cM `*.glimpse.map`

#5 minimac_map tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`${prefix}.minimac.map` file	File containing the map in Minimac format: tab-delimited file with header and columns: chr, pos, cM `*.minimac.map`

Tool	Description	Homepage
custom	Custom script to convert any genetic map format	https://github.com/nf-core/tools

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:33:53 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcustom%2Fgeneticmapconvert/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/custom/geneticmapconvert/blobs/sha256:83ec351cd7b59ef3e7442b5af981f44f2c2e9a74ea053144a0cc4d5fd6b66e53
Size	8.1 KB
Checksum	sha256:83ec351cd7b59ef3e7442b5af981f44f2c2e9a74ea053144a0cc4d5fd6b66e53
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:33:53 (UTC)		1	8.1 KB	-