Nextflow Registry | nf-core/custom/geneticmapconvert@0.0.0-3fc6d40

nf-core/custom/geneticmapconvert @ 0.0.0-3fc6d40

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: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:08:27 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcustom%2Fgeneticmapconvert/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/custom/geneticmapconvert/blobs/sha256:7eab753bb1ec88b03ae35e6b235eafd50b366be8c9a731aa267c99454b452b14
Size	8.1 KB
Checksum	sha256:7eab753bb1ec88b03ae35e6b235eafd50b366be8c9a731aa267c99454b452b14
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:12:07 (UTC)	3	8.0 KB
0.0.0-3fc6d40	22 Apr 2026 15:08:27 (UTC)	3	8.1 KB
0.0.0-0c7146d	08 Apr 2026 18:55:12 (UTC)	4	8.1 KB