modules/custom_geneticmapconvert

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

mapconvertionR

https://github.com/nf-core/modules/[...]/modules/nf-core/custom/geneticmapconvert

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`glimpse_map`

`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

`plink_map`

`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

`stitch_map`

`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

`minimac_map`

`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

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

`session_info`

`meta`
`:map`

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

`${prefix}.R_sessionInfo.log`
`:file`

dump of R SessionInfo

*.log

Topics

name:type

description

pattern

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

custom
MIT

Custom script to convert any genetic map format

github.com/nf-core/tools

modules/custom_geneticmapconvert

Description

Input

`meta`
`:map`

`map_file`
`:file`

Output

`glimpse_map`

`meta`
`:map`

`${prefix}.glimpse.map`
`:file`

`plink_map`

`meta`
`:map`

`${prefix}.plink.map`
`:file`

`stitch_map`

`meta`
`:map`

`${prefix}.stitch.map`
`:file`

`minimac_map`

`meta`
`:map`

`${prefix}.minimac.map`
`:file`

`versions`

`versions.yml`
`:file`

`session_info`

`meta`
`:map`

`${prefix}.R_sessionInfo.log`
`:file`

Topics

`versions`

`versions.yml`
`:file`

Tools

custom
MIT

maintainer

get in touch

modules/custom_geneticmapconvert

Description

Input

meta:map

map_file:file

Output

glimpse_map

meta:map

${prefix}.glimpse.map:file

plink_map

meta:map

${prefix}.plink.map:file

stitch_map

meta:map

${prefix}.stitch.map:file

minimac_map

meta:map

${prefix}.minimac.map:file

versions

versions.yml:file

session_info

meta:map

${prefix}.R_sessionInfo.log:file

Topics

versions

versions.yml:file

Tools

custom MIT

maintainer

get in touch

`meta`
`:map`

`map_file`
`:file`

`glimpse_map`

`meta`
`:map`

`${prefix}.glimpse.map`
`:file`

`plink_map`

`meta`
`:map`

`${prefix}.plink.map`
`:file`

`stitch_map`

`meta`
`:map`

`${prefix}.stitch.map`
`:file`

`minimac_map`

`meta`
`:map`

`${prefix}.minimac.map`
`:file`

`versions`

`versions.yml`
`:file`

`session_info`

`meta`
`:map`

`${prefix}.R_sessionInfo.log`
`:file`

`versions`

`versions.yml`
`:file`

custom
MIT