Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit 6b7c7e02 authored by Louis Duchemin's avatar Louis Duchemin
Browse files

Gemma pipeline for relatedness matrix

parent 8c0cd86d
open Core_kernel
open Bistro
open Bistro.Shell_dsl
class type relatedness_matrix = object
inherit text
method format : [`gemma_relatedness_matrix]
end
let%pworkflow genotype_of_fasta fasta =
let module G = Reviewphiltrans_toolbox.Gemma in
G.write_genotypes ~alignment:[%path fasta] ~output:[%dest]
let template_of_mode m =
int (
match m with
| `Centered -> 1
| `Standardized -> 2
)
let calculate_relatedness_matrix ~mode ~genotype ~phenotype =
Workflow.shell ~descr:"gemma.calculate_relatedness_matrix" [
cmd "gemma" [
opt "-g" dep genotype ;
opt "-p" dep phenotype ;
opt "-gk" template_of_mode mode ;
opt "-o" Fn.id dest ;
]
]
\ No newline at end of file
open Bistro
open File_formats
class type relatedness_matrix = object
inherit text
method format : [`gemma_relatedness_matrix]
end
val genotype_of_fasta : aminoacid_fasta file -> bimbam file
val calculate_relatedness_matrix :
mode:[`Centered | `Standardized] ->
genotype:bimbam file ->
phenotype:bimbam file ->
relatedness_matrix file
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