Commit 196d70d8 authored by hjulienne's avatar hjulienne

local example pipeline

parent 3c67f259
params.compute_project=true
params.compute_LDSC_matrix=true
params.compute_imputation=true
params.compute_imputation=false
params.meta_data = "${baseDir}"+"/input_files/test_final.csv"
params.gwas_folder = "/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/"
params.meta_data = "${baseDir}"+"/input_files/test_meta.csv"
params.gwas_folder = ""
params.ref_panel = '/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel/'
params.group = "${baseDir}/input_files/group.txt"
......@@ -33,7 +33,6 @@ generate_trait_pairs_channel = Channel.fromPath("${baseDir}/generate_trait_pairs
parse_correlation_channel = Channel.fromPath("${baseDir}/parse_correlation_results.py")
process Compute_MAF{
input:
file ref_panel from ref_chr_channel3.collect()
......
......@@ -20,7 +20,7 @@ singularity {
}
process{
executor='slurm'
executor='local'
maxErrors=10
maxRetries=3
maxForks=400
......@@ -29,14 +29,13 @@ process{
cache='deep'
withName: 'Compute_MAF' {
container='plink_1.90b5--heea4ae3_0.sif'
cpus=1
}
withName: 'Compute_MAF' {
container='docker://quay.io/biocontainers/plink:1.90b5--heea4ae3_1'
cpus=1
}
//docker://quay.io/biocontainers/jass_preprocessing:1.0--py_0
withName: 'create_WG_reference_panel' {
container='jass_preprocessing_2.0--py_0.sif'
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
cpus=1
}
......@@ -45,42 +44,42 @@ process{
}
withName: 'Clean_GWAS' {
// container='jass_preprocessing_2.0--py_0.sif'
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
cpus=1
}
withName: 'Impute_GWAS' {
container="raiss_2.0--py_0.sif"
container="docker://quay.io/biocontainers/raiss_2.0--py_0"
cpus=1
}
withName: 'Munge_LDSC_data' {
container='ldsc_1.0.1--py_0.sif'
container='docker://quay.io/biocontainers/ldsc_1.0.1--py_0'
cpus=1
}
withName: 'Generate_trait_pair' {
container='jass_preprocessing_2.0--py_0.sif'
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
cpus=1
}
withName: 'Correlation_LDSC_data' {
container="ldsc_1.0.1--py_0.sif"
container="docker://quay.io/biocontainers/ldsc_1.0.1--py_0.sif"
cpus=1
}
withName: 'Correlation_matrices' {
container='jass_preprocessing_2.0--py_0.sif'
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
cpus=1
}
withName: 'Create_inittable_LDSC' {
container='jass_2.0--pyh5ca1d4c_0.sif'
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
withName: 'Create_inittable' {
container='jass_2.0--pyh5ca1d4c_0.sif'
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
......@@ -89,7 +88,7 @@ process{
}
withName: 'Create_project_data' {
container='jass_2.0--pyh5ca1d4c_0.sif'
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
......
......@@ -25,17 +25,18 @@ process{
maxRetries=3
maxForks=400
queueSize=500
errorStrategy='retry'
errorStrategy='finish'
cache='deep'
withName: 'Compute_MAF' {
container='docker://quay.io/biocontainers/plink_1.90b5--heea4ae3_0'
container='plink_1.90b5--heea4ae3_0.sif'
cpus=1
}
//docker://quay.io/biocontainers/jass_preprocessing:1.0--py_0
withName: 'create_WG_reference_panel' {
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
container='jass_preprocessing_2.0--py_0.sif'
cpus=1
}
......@@ -44,42 +45,42 @@ process{
}
withName: 'Clean_GWAS' {
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
// container='jass_preprocessing_2.0--py_0.sif'
cpus=1
}
withName: 'Impute_GWAS' {
container="docker://quay.io/biocontainers/raiss_2.0--py_0"
container="raiss_2.0--py_0.sif"
cpus=1
}
withName: 'Munge_LDSC_data' {
container='docker://quay.io/biocontainers/ldsc_1.0.1--py_0'
container='ldsc_1.0.1--py_0.sif'
cpus=1
}
withName: 'Generate_trait_pair' {
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
container='jass_preprocessing_2.0--py_0.sif'
cpus=1
}
withName: 'Correlation_LDSC_data' {
container="docker://quay.io/biocontainers/ldsc_1.0.1--py_0.sif"
container="ldsc_1.0.1--py_0.sif"
cpus=1
}
withName: 'Correlation_matrices' {
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
container='jass_preprocessing_2.0--py_0.sif'
cpus=1
}
withName: 'Create_inittable_LDSC' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
container='jass_2.0--pyh5ca1d4c_0.sif'
cpus=1
}
withName: 'Create_inittable' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
container='jass_2.0--pyh5ca1d4c_0.sif'
cpus=1
}
......@@ -88,7 +89,7 @@ process{
}
withName: 'Create_project_data' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
container='jass_2.0--pyh5ca1d4c_0.sif'
cpus=1
}
......
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