diff --git a/Ref_Panel/1000G_AMR_0_01.csv b/Ref_Panel/1000G_AMR_0_01.csv
index 73ba86a44757d3639b6fa506698ab60ce6adb4f8..8517b1b84654f4b2357560d32ca1e78526789b6f 100755
Binary files a/Ref_Panel/1000G_AMR_0_01.csv and b/Ref_Panel/1000G_AMR_0_01.csv differ
diff --git a/Ref_Panel/1000G_EAS_0_01.csv b/Ref_Panel/1000G_EAS_0_01.csv
old mode 100755
new mode 100644
index 83ab685c2be8a4bd213ad117ab991b01600d6f0a..fb62efacb3efe39254248a5285f9a696aeb40a4e
Binary files a/Ref_Panel/1000G_EAS_0_01.csv and b/Ref_Panel/1000G_EAS_0_01.csv differ
diff --git a/Ref_Panel/1000G_EUR_0_01.csv b/Ref_Panel/1000G_EUR_0_01.csv
index fbe934a21450750c9ff6e2d5ae4f42208f1d02a2..44d786177f9c6b6ca56f0f79753640021af39bd1 100755
Binary files a/Ref_Panel/1000G_EUR_0_01.csv and b/Ref_Panel/1000G_EUR_0_01.csv differ
diff --git a/Ref_Panel/1000G_SAS_0_01.csv b/Ref_Panel/1000G_SAS_0_01.csv
index 9a1a90f163af7513e5b9295eec3754d263f750a5..52db85218eeb10bd8be57ca2584ff77a3af68527 100755
Binary files a/Ref_Panel/1000G_SAS_0_01.csv and b/Ref_Panel/1000G_SAS_0_01.csv differ
diff --git a/jass_pipeline_v2.nf b/jass_pipeline_v2.nf
index 4f59204f4498a3040343239dea5a0d809e044fdb..3001e340a18907d4075f888ffa9af637590af53d 100644
--- a/jass_pipeline_v2.nf
+++ b/jass_pipeline_v2.nf
@@ -9,16 +9,17 @@ nextflow.enable.dsl=2
/* Parameter to set if optional pipeline steps are performed */
params.compute_project=true // Compute JASS runs
params.compute_LDSC_matrix=false // Infer the genetic covariance and residual covariance using the LDscore regression (Bulik-Sullivan, et al, 2015). The residual covariance is necessary to perform multi-trait GWAS (see julienne, et al 2021) If set to false, the residual covariance will be infered from Zscores
-params.compute_imputation=true
+params.compute_imputation=false
/* Path of input data */
-params.meta_data = "${projectDir}"+"/input_files/Data_test_EAS_1_sumstat.csv" // file describing gwas summary statistic format
+params.meta_data = "${projectDir}"+"/input_files/Data_test_EAS.csv" // file describing gwas summary statistic format
params.gwas_folder = "${projectDir}" + "/test_data/hg38_EAS/"
// //"/pasteur/zeus/projets/p02/GGS_JASS/1._DATA/Summary_stat_hg38/EAS/"
params.region = Channel.fromPath("${projectDir}"+"/input_files/All_Regions_ALL_ensemble_1000G_hg38_EAS.bed")
-params.ref_panel_WG = "${projectDir}"+"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv"//"${projectDir}/Ref_Panel/1000G_SAS_0_01_chr22.csv"
+params.ref_panel_WG = "${projectDir}"+"/Ref_Panel/1000G_EAS_0_01_chr22_21.csv"
+//"${projectDir}/Ref_Panel/1000G_SAS_0_01_chr22.csv"
params.ancestry="EAS"
params.prefix="ALL_ensemble_1000G_hg38_EAS_chr"
@@ -41,84 +42,111 @@ params.diagnostic_folder= "/pasteur/zeus/projets/p02/GGS_JASS/jass_pipeline_dev_
params.r2threshold = 0.6
params.eigenthreshold = 0.05
params.minimumld = 5
+params.ld_type = "plink"
params.ld_folder = Channel.fromPath("/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/Matrix_LD_RAISS/EAS/*.ld").collect()
params.ref_panel = '/pasteur/zeus/projets/p02/GGS_WKD/DATA_1000G/Panels/EAS/'
chr_channel = Channel.from(21..22)
params.ref_chr_path= Channel.fromPath(params.ref_panel+"/ALL_ensemble_1000G_hg38_EAS_chr*.bim").collect()
+params.perform_sanity_checks=true
+params.perform_accuracy_checks=true
-// /* Project group */
-// params.group = "${projectDir}/input_files/group.txt"
-// group = file(params.group)
-
-// /* Generate channel from path */
-// Region_channel = Channel.fromPath(params.region)
-
-// extract_sample_size_script_channel = Channel.fromPath("${projectDir}/bin/extract_sample_size.py")
-// generate_trait_pairs_channel = Channel.fromPath("${projectDir}/bin/generate_trait_pairs.py")
-// parse_correlation_channel = Channel.fromPath("${projectDir}/bin/parse_correlation_results.py")
+/* Project group */
+params.group = "${projectDir}/input_files/group.txt"
+group = file(params.group)
+extract_sample_size_script_channel = "${projectDir}/bin/extract_sample_size.py"
+generate_trait_pairs_channel = "${projectDir}/bin/generate_trait_pairs.py"
+parse_correlation_channel = "${projectDir}/bin/parse_correlation_results.py"
/*****************************/
/* process inclusion */
/*****************************/
-
include {Meta_data_GWAS; Clean_GWAS} from "./modules/Clean_GWAS"
include {Impute_GWAS} from "./modules/RAISS_imputation"
include {Perf_RAISS; Sanity_Checks_RAISS; Put_in_harmonized_folder; Put_in_imputed_folder} from "./modules/RAISS_sanity_checks"
-// include {Munge_LDSC_data; Heritability_LDSC_data; Correlation_LDSC_data; Generate_trait_pair;Parsing_correlation_matrices} from "./modules/LDSC"
-// include {Create_inittable_LDSC} from "./modules/JASS"
+include {Munge_LDSC_data; Heritability_LDSC_data;Generate_trait_pair; Correlation_LDSC_data;Parsing_correlation_matrices} from "./modules/LDSC" //; Generate_trait_pair;
+include {Create_inittable_LDSC; Create_inittable; Get_pheno_group; Create_project_data} from "./modules/JASS"
/*******************************/
workflow{
/****** PREPROCESSING ******/
- Meta_data_GWAS()
+ Meta_data_GWAS(params.meta_data)
Clean_GWAS(params.ref_panel_WG, Meta_data_GWAS.out.flatten())
- // /****** IMPUTATION ******/
- Impute_GWAS(Clean_GWAS.out.cleaned_gwas_chr_channel.flatten(), params.ref_chr_path.collect(), params.ld_folder.collect())
-
- sanity_cleaned_in_folder = Put_in_harmonized_folder(Clean_GWAS.out.cleaned_gwas_chr_channel.collect())
- sanity_imputed_in_folder = Put_in_imputed_folder(Impute_GWAS.out.imputed_gwas_channel.collect())
-
- Clean_GWAS.out.cleaned_gwas_chr_channel
- .map {it.name.toString().split('_chr')[0]}
- .unique()
- .view()
-
- chr_channel
- .max()
- .map{it + 1}
- .set {chr_max}
-
- chr_channel
- .min()
- .set {chr_min}
-
- Clean_GWAS.out.cleaned_gwas_chr_channel.flatten()
- .map {(it.name.toString() =~ /(z_[0-9A-Za-z-]+_[0-9A-Za-z-]+)/ )[0][1]}
- .view()
-
- Clean_GWAS.out.cleaned_gwas_chr_channel
- .map {(it.name.toString() =~ /(z_[0-9A-Za-z-]+_[0-9A-Za-z-]+)/ )[0][1]}
- .unique()
- .set {trait_channel}
-
-
- Sanity_Checks_RAISS(sanity_cleaned_in_folder.collect(), sanity_imputed_in_folder.collect(), trait_channel, chr_min, chr_max)
-
- //, chr_channel.min(), chr_channel.max()+1)
- //Perf_RAISS(Clean_GWAS.out.cleaned_gwas_chr_channel.filter("*_chr22.txt").flatten(), params.ref_chr_path.collect(), params.ld_folder.collect())
-
- // /****** Genetic variance ******/
- // Munge_LDSC_data(Clean_GWAS.out.cleaned_gwas_channel.flatten())
- // Heritability_LDSC_data(Munge_LDSC_data.out.ldsc_data_channel)
- // Generate_trait_pair(generate_trait_pairs_channel, Munge_LDSC_data.out.ldsc_data_channel.collect())
- // Correlation_LDSC_data(Generate_trait_pair.out.flatten(), Munge_LDSC_data.out.ldsc_data_channel.collect())
- // Parsing_correlation_matrices(parse_correlation_channel, Correlation_LDSC_data.out.cor_log_channel, Heritability_LDSC_data.out.h2_log_channel)
-
- // /****** JASS Inittable *****/
-
- // Create_inittable_LDSC(Impute_GWAS.out.imputed_gwas_channel, Clean_GWAS.out.cleaned_gwas_channel, Parsing_correlation_matrices.out.cov_H0_matrice_channel, Parsing_correlation_matrices.out.cov_gen_matrice_channel, params.region)
-
+ /******** IMPUTATION *******/
+ if(params.compute_imputation){
+
+ Impute_GWAS(Clean_GWAS.out.cleaned_gwas_chr_channel.flatten(), params.ref_chr_path.collect(), params.ld_folder.collect())
+
+ sanity_cleaned_in_folder = Put_in_harmonized_folder(Clean_GWAS.out.cleaned_gwas_chr_channel.collect())
+ sanity_imputed_in_folder = Put_in_imputed_folder(Impute_GWAS.out.imputed_gwas_channel.collect())
+
+ chr_channel
+ .max()
+ .map{it + 1}
+ .set {chr_max}
+
+ chr_channel
+ .min()
+ .set {chr_min}
+
+ Clean_GWAS.out.cleaned_gwas_chr_channel
+ .map {(it.name.toString() =~ /(z_[0-9A-Za-z-]+_[0-9A-Za-z-]+)/ )[0][1]}
+ .unique()
+ .set {trait_channel}
+
+ Clean_GWAS.out.cleaned_gwas_chr_channel.flatten().filter( ~/.*z.*chr22\.txt/ ).view()
+ if(params.perform_accuracy_checks){
+ Perf_RAISS(Clean_GWAS.out.cleaned_gwas_chr_channel.flatten().filter( ~/.*z.*_chr22\.txt/ ), params.ref_chr_path.collect(), params.ld_folder.collect())
+ //Perf_RAISS(Clean_GWAS.out.cleaned_gwas_chr_channel.collect(), params.ref_chr_path.collect(), params.ld_folder.collect())
+ }
+
+ if(params.perform_sanity_checks){
+ Sanity_Checks_RAISS(sanity_cleaned_in_folder.collect(), sanity_imputed_in_folder.collect(), trait_channel, chr_min, chr_max)
+ }
+ }
+
+ // /****** Genetic variance and corresponding inittable ******/
+
+ if(params.compute_LDSC_matrix){
+ Munge_LDSC_data(Clean_GWAS.out.cleaned_gwas_channel.flatten())
+ Heritability_LDSC_data(Munge_LDSC_data.out.ldsc_data_channel)
+ Generate_trait_pair(generate_trait_pairs_channel, Munge_LDSC_data.out.ldsc_data_channel.collect())
+ Correlation_LDSC_data(Generate_trait_pair.out.flatten(), Munge_LDSC_data.out.ldsc_data_channel.collect())
+ Parsing_correlation_matrices(parse_correlation_channel, Correlation_LDSC_data.out.cor_log_channel, Heritability_LDSC_data.out.h2_log_channel)
+
+ // /****** JASS Inittable with LDSC covariance matrix (preferred method)*****/
+ if(params.compute_imputation){
+ Create_inittable_LDSC(Impute_GWAS.out.imputed_gwas_channel.collect(), Clean_GWAS.out.cleaned_gwas_channel.collect(), Parsing_correlation_matrices.out.cov_H0_matrice_channel, Parsing_correlation_matrices.out.cov_gen_matrice_channel, params.region)
+ }
+ else{
+ Create_inittable_LDSC(Clean_GWAS.out.cleaned_gwas_chr_channel.collect(), Clean_GWAS.out.cleaned_gwas_channel.collect(), Parsing_correlation_matrices.out.cov_H0_matrice_channel, Parsing_correlation_matrices.out.cov_gen_matrice_channel, params.region)
+ }
+
+ /*Compute multi-trait GWAS*/
+ if(params.compute_project){
+ Get_pheno_group(params.group)
+ Create_project_data(Get_pheno_group.out.pheno_group, Create_inittable_LDSC.out.init_table)
+ //Create_project_data.out.result.view()
+ }
+ }
+ else {
+ if(params.compute_imputation){
+ Create_inittable(Impute_GWAS.out.imputed_gwas_channel.collect(), Clean_GWAS.out.cleaned_gwas_channel.collect(), params.region)
+ }
+ else{
+ Create_inittable(Clean_GWAS.out.cleaned_gwas_chr_channel.collect(), Clean_GWAS.out.cleaned_gwas_channel.collect(), params.region)
+ }
+
+
+
+ /*Compute multi-trait GWAS*/
+ if(params.compute_project){
+ Get_pheno_group(params.group)
+ Get_pheno_group.out.pheno_group.flatten().view()
+ Create_project_data(Get_pheno_group.out.pheno_group.collect(), Create_inittable.out.init_table_channel_no_ldsc)
+ //Create_project_data.out.result.view()
+ }
+ }
}
\ No newline at end of file
diff --git a/modules/Clean_GWAS.nf b/modules/Clean_GWAS.nf
index ceee03e6de474351cb28dbfce75edc4855587145..962ef2c3fb149b4fa2ee334ad387e1c7c03b1de7 100644
--- a/modules/Clean_GWAS.nf
+++ b/modules/Clean_GWAS.nf
@@ -1,15 +1,17 @@
process Meta_data_GWAS{
+ input:
+ path pheno_list
output:
path "meta_data_chk*.csv"
"""
- d=`wc -l ${params.meta_data}`
+ d=`wc -l ${pheno_list}`
e=`echo \$d | cut -d ' ' -f 1`
for ((i = 2; i <= \$e; i++));
do
- head -n1 ${params.meta_data} > "meta_data_chk\$i.csv"
- head -n \$i ${params.meta_data} | tail -n 1 >> "meta_data_chk\$i.csv"
+ head -n1 ${pheno_list} > "meta_data_chk\$i.csv"
+ head -n \$i ${pheno_list} | tail -n 1 >> "meta_data_chk\$i.csv"
done
"""
}
diff --git a/modules/JASS.nf b/modules/JASS.nf
index 5aa566685f49eedfb2d773d3f0b1bd09aa7d5ca7..1ac35dedc9fe60d0602a64a3c89d11164a3d47b6 100644
--- a/modules/JASS.nf
+++ b/modules/JASS.nf
@@ -1,19 +1,14 @@
process Create_inittable_LDSC {
publishDir "${params.output_folder}/init_table/", pattern: "*.hdf5", mode: 'copy'
- memory {16.GB * task.attempt}
- time {24.h * task.attempt}
- queue 'dedicated,common,ggs'
input:
- path cleaned_gwas_chr //from imputed_gwas_channel.mix(not_imputed_gwas_channel).unique().collect()
- path cleaned_gwas //from cleaned_gwas_channel2.collect()
- path Covariance_H0 //from cov_H0_matrice_channel
- path Covariance_gen //from cov_gen_matrice_channel
- path Regions //from Region_channel
+ path cleaned_gwas_chr
+ path cleaned_gwas
+ path Covariance_H0
+ path Covariance_gen
+ path Regions
output:
- path "*.hdf5", emit: init_table_channel
- when:
- params.compute_LDSC_matrix
+ path "*.hdf5", emit: init_table
"""
gwas_list_str=`echo ${cleaned_gwas} | sed s'/.txt//'g`
@@ -26,76 +21,60 @@ process Create_inittable_LDSC {
"""
}
+process Create_inittable {
+ publishDir "${params.output_folder}/init_table/", pattern: "*.hdf5", mode: 'copy'
+ input:
+ path cleaned_gwas_chr
+ path cleaned_gwas
+ path Regions
+ output:
+ path "*.hdf5", emit: init_table_channel_no_ldsc
+ """
+ gwas_list_str=`echo ${cleaned_gwas} | sed s'/.txt//'g`
+ echo \$gwas_list_str
+ date_init=\$(date +"%m_%d_%Y-%H:%M")
-// process Create_inittable {
-
-// publishDir "${params.output_folder}/init_table/", pattern: "*.hdf5", mode: 'copy'
-// memory {16.GB * task.attempt}
-// time {24.h * task.attempt}
-
-// input:
-// path cleaned_gwas_chr from imputed_gwas_channel2.mix(not_imputed_gwas_channel2).unique().collect()
-// path cleaned_gwas from cleaned_gwas_channel3.collect()
-// path Regions from Region_channel2
-// output:
-// path "*.hdf5", emit: init_table_channel_no_ldsc
-// when:
-// !params.compute_LDSC_matrix
-// """
-
-// gwas_list_str=`echo ${cleaned_gwas} | sed s'/.txt//'g`
-// echo \$gwas_list_str
-// date_init=\$(date +"%m_%d_%Y-%H:%M")
-
-// init_name="inittable_NO_LDSC_\$date_init.hdf5"
-// jass create-inittable --input-data-path "./*.txt" --regions-map-path ${Regions} --description-file-path ${params.meta_data} --init-table-path \$init_name
-
-// """
-// }
-
-
-// //
-// // Generate one list of phenotype
-// //
-// process get_pheno_group {
-// input:
-// path 'group.txt' from group
-// output:
-// path "pheno_group_*" into pheno_group_channel
-// when:
-// params.compute_project
-// """
-// split -l 1 group.txt pheno_group_
-// """
-// }
-
-// process Create_project_data {
-// publishDir "${projectDir}/worktable/", pattern:"worktable_*.hdf5", mode: 'move'
-// publishDir "${projectDir}/quadrant/", pattern:"quadrant_*.png", mode: 'move'
-// publishDir "${projectDir}/manhattan/", pattern:"manhattan_*.png", mode: 'move'
+ init_name="inittable_NO_LDSC_\$date_init.hdf5"
+ jass create-inittable --input-data-path "./*.txt" --regions-map-path ${Regions} --description-file-path ${params.meta_data} --init-table-path \$init_name
-// input:
-// path pheno_group from pheno_group_channel.collect()
-// path init_table from init_table_channel.mix(init_table_channel_no_ldsc)
+ """
+}
-// output:
-// path "worktable*.hdf5", emit: worktable_channel
-// path "*.png", emit: plot_channel
-// stdout result
+//
+// Generate one list of phenotype
+//
+process Get_pheno_group {
+ input:
+ path group
+ output:
+ path "pheno_group_*", emit: pheno_group
+ """
+ split -l 1 ${group} pheno_group_
+ """
+}
-// when:
-// params.compute_project
-// """
-// for pheno_line in ${pheno_group}
-// do
-// echo \$pheno_line
-// group_tag="\$(cat \$pheno_line | cut -d';' -f1)"
-// pheno_list="\$(cat \$pheno_line | cut -d';' -f2)"
+process Create_project_data {
+ publishDir "${params.output_folder}/worktable/", pattern:"worktable_*.hdf5", mode: 'copy'
+ publishDir "${params.output_folder}/quadrant/", pattern:"quadrant_*.png", mode: 'copy'
+ publishDir "${params.output_folder}/manhattan/", pattern:"manhattan_*.png", mode: 'copy'
+ input:
+ path pheno_group
+ path init_table
+ output:
+ path "worktable_*.hdf5", emit: worktables
+ path "quadrant_*.png", emit: quadrant
+ path "manhattan_*.png", emit: manhattan
+ """
+ for pheno_line in ${pheno_group}
+ do
+ echo \$pheno_line
+ group_tag="\$(cat \$pheno_line | cut -d';' -f1)"
+ pheno_list="\$(cat \$pheno_line | cut -d';' -f2)"
-// echo \$group_tag
-// echo \$pheno_list
+ echo \$group_tag
+ echo \$pheno_list
-// jass create-project-data --phenotypes \$pheno_list --init-table-path ./${init_table} --worktable-path ./worktable_bis_\$group_tag.hdf5 --manhattan-plot-path ./manhattan_\$group_tag.png --quadrant-plot-path ./quadrant_\$group_tag.png
-// done
-// """
-// }
\ No newline at end of file
+ jass create-project-data --phenotypes \$pheno_list --init-table-path ./${init_table} --worktable-path ./worktable_bis_\$group_tag.hdf5 --manhattan-plot-path ./manhattan_\$group_tag.png --quadrant-plot-path ./quadrant_\$group_tag.png
+ done
+ """
+}
\ No newline at end of file
diff --git a/modules/LDSC.nf b/modules/LDSC.nf
index 3db538f89df3696fccc876bd4620bb0fc1c42b25..d690536bdd0a8a6eb5109ba28ec69ddd681042b9 100644
--- a/modules/LDSC.nf
+++ b/modules/LDSC.nf
@@ -2,9 +2,7 @@
process Munge_LDSC_data {
publishDir "${params.output_folder}", pattern: "ldsc_data/data_*.sumstats.gz", mode: 'copy'
publishDir "${params.output_folder}", pattern: "ldsc_data/*.log", mode: 'copy'
- time = {1.h * task.attempt}
- maxRetries = 4
- queue 'dedicated,common,ggs'
+
input:
path clean_gwas
output:
@@ -27,31 +25,30 @@ process Munge_LDSC_data {
"""
}
-process Generate_trait_pair {
- time '1h'
- queue 'dedicated,common,ggs'
+process Heritability_LDSC_data {
+
+ publishDir "${params.output_folder}/h2_data/", pattern: "*.log", mode: 'copy'
input:
- path generate_trait_pairs_script
path ldsc_data
output:
- path "pairs_chunk_*.txt",emit: combi_channel
+ path "*.log", emit: h2_log_channel
"""
- python3 ${generate_trait_pairs_script}
+ my_trait=\$(ls ${ldsc_data} | cut -d "_" -f2,3 | cut -d '.' -f1)
+ ldsc.py --h2 ${ldsc_data} --ref-ld-chr ${params.LD_SCORE_folder}${params.prefix}@ --w-ld-chr ${params.LD_SCORE_folder}${params.prefix}@ --out \${my_trait}
"""
}
-process Heritability_LDSC_data {
- memory {8.GB * task.attempt}
- time {24.h * task.attempt}
+
+process Generate_trait_pair {
+ time '1h'
queue 'dedicated,common,ggs'
- publishDir "${params.output_folder}/h2_data/", pattern: "*.log", mode: 'copy'
input:
+ path generate_trait_pairs_script
path ldsc_data
output:
- path "*.log", emit: h2_log_channel
+ path "pairs_chunk_*.txt",emit: combi_channel
"""
- my_trait=\$(ls ${ldsc_data} | cut -d "_" -f2,3 | cut -d '.' -f1)
- ldsc.py --h2 ${ldsc_data} --ref-ld-chr ${params.LD_SCORE_folder}${params.prefix}@ --w-ld-chr ${params.LD_SCORE_folder}${params.prefix}@ --out \${my_trait}
+ python3 ${generate_trait_pairs_script}
"""
}
@@ -59,7 +56,7 @@ process Heritability_LDSC_data {
process Correlation_LDSC_data {
memory {8.GB * task.attempt}
time {24.h * task.attempt}
- queue 'dedicated,common,ggs'
+
publishDir "${params.output_folder}/cor_data/", pattern: "*.log", mode: 'copy'
input:
path trait_pair
diff --git a/modules/RAISS_sanity_checks.nf b/modules/RAISS_sanity_checks.nf
index 20319e6de8a1d6bc8d35cf84c071e601b409555a..e08dc1016044909168dded160e5be72acfe095b5 100755
--- a/modules/RAISS_sanity_checks.nf
+++ b/modules/RAISS_sanity_checks.nf
@@ -1,14 +1,14 @@
process Perf_RAISS {
publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
- publishDir "${params.output_folder}/RAISS_Performance_reports/", pattern: "Perf_*", mode: 'copy'
+ publishDir "${params.output_folder}", pattern: "raiss_report/perf_report_*", mode: 'copy'
input:
- file gwas_files
- file ref_file
- file ld_file
+ path gwas_files
+ path ref_file
+ path ld_file
script:
"""
- mkdir -p imputed_gnomad
+ mkdir -p imputed_GWAS
mkdir -p masked_zscore
mkdir -p raiss_report
chrom=\$(echo ${gwas_files} | cut -d '_' -f4 | cut -d "." -f1)
@@ -17,7 +17,7 @@ process Perf_RAISS {
echo \$chrom
echo \$study
- raiss --ld-folder ./ --ref-folder ./ --gwas \$study --chrom chr22 --ld-type scipy performance-grid-search --harmonized-folder ./ --masked-folder ./masked_zscore/ --imputed-folder ./imputed_gnomad/ --output-path ./raiss_report --eigen-ratio-grid '[${params.eigenthreshold}]' --ld-threshold-grid '[${params.r2threshold}]' --n-cpu 8
+ raiss --ld-folder ./ --ref-folder ./ --gwas \$study --chrom chr22 --ld-type ${params.ld_type} --ref-panel-prefix ${params.prefix_Impute_GWAS} --ref-panel-suffix ${params.suffix}.bim performance-grid-search --harmonized-folder ./ --masked-folder ./masked_zscore/ --imputed-folder ./imputed_GWAS/ --output-path ./raiss_report --eigen-ratio-grid '[${params.eigenthreshold}]' --ld-threshold-grid '[${params.r2threshold}]' --n-cpu 1
"""
}
diff --git a/nextflow_slurm.config b/nextflow_slurm.config
index eefb5b0f12c3e44b454a1548c3e7a69c9892efd2..47c22e0f789493666e792675c4896ca12e384dcc 100644
--- a/nextflow_slurm.config
+++ b/nextflow_slurm.config
@@ -67,24 +67,38 @@ process{
cpus=1
}
+ withName: 'Perf_RAISS' {
+ memory={8.GB * task.attempt}
+ time={72.h * task.attempt}
+ maxRetries=4
+ queue='dedicated,ggs,common'
+ cpus=1
+ }
+
withName: 'Munge_LDSC_data' {
container='ldsc_1.0.1--py_0.sif'
cpus=1
+ time={1.h * task.attempt}
+ maxRetries=4
+ queue='dedicated,common,ggs'
}
withName: 'Generate_trait_pair' {
- container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
- cpus=1
+ container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
+ cpus=1
}
withName: 'Heritability_LDSC_data' {
- container="ldsc_1.0.1--py_0.sif"
- cpus=1
+ memory={8.GB * task.attempt}
+ time={24.h * task.attempt}
+ queue='dedicated,common,ggs'
+ container="ldsc_1.0.1--py_0.sif"
+ cpus=1
}
withName: 'Correlation_LDSC_data' {
container="ldsc_1.0.1--py_0.sif"
- cpus=1
+ cpus=1
}
withName: 'Parsing_correlation_matrices' {
@@ -93,11 +107,15 @@ process{
}
withName: 'Create_inittable_LDSC' {
- cpus=1
+ memory={16.GB * task.attempt}
+ time={24.h * task.attempt}
+ cpus=1
}
withName: 'Create_inittable' {
- cpus=1
+ memory={16.GB * task.attempt}
+ time={24.h * task.attempt}
+ cpus=1
}
withName: 'get_pheno_group' {