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nf-core/plink/recode @ 0.0.0-6c4ed3a

Recodes plink bfiles into a new text fileset applying different modifiers

recode bfiles plink whole genome association
Latest version: 0.0.0-6c4ed3a
Total downloads: 13
Source: nf-core/modules
Authors: @atrigila
Maintainers: @atrigila

Summary

Recodes plink bfiles into a new text fileset applying different modifiers

Get started

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

include { PLINK_RECODE } from 'nf-core/plink/recode'

License

MIT License

Process
Name PLINK_RECODE
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bed file

PLINK binary biallelic genotype table file

 *.{bed}
bim file

PLINK extended MAP file

 *.{bim}
fam file

PLINK sample information file

 *.{fam}
Output 25 channels
#1 gen tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.gen file

Oxford genotype file format. Produced by "--recode oxford".

 *.{gen}
#2 map tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.map file

PLINK text fileset variant information file. Produced by the default "--recode" or by "--recode 12".

 *.{map}
#3 ped tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.ped file

PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default "--recode" or by "--recode 12".

 *.{ped}
#4 pos tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.recode.pos.txt file

BIMBAM variant position file. Produced by "--recode bimbam".

 *.{recode.pos.txt}
#5 raw tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.raw file

Additive + dominant component file. Produced by "--recode AD" or "--recode A".

 *.{raw}
#6 txt tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.txt file

Text file. Produced by "--recode 23". Can only be used in a file with only one sample.

 *.{txt}
#7 vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.vcf file

Variant calling file (VCF). Produced by "--recode vcf".

 *.{vcf}
#8 geno tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.recode.geno.txt file

BIMBAM genotype file. Produced by "--recode bimbam".

 *.{recode.geno.txt}
#9 info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.info file

Haploview map file. Produced by "--recode HV".

 *.{info}
#10 lgen tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.lgen file

PLINK long-format genotype file. Produced by "--recode lgen".

 *.{lgen}
#11 list tuple
meta map

Groovy Map containing sample information e.g.