Commit 61fd47df authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

updated tutorial data

parent 84bf3b6e
......@@ -9,13 +9,13 @@ chr_channel = Channel.from(1..22)
ref_chr_channel=Channel.fromPath(params.ref_panel+"/chr*.eur.1pct.bim")
ld_channel=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/WKD_Hanna/impute_for_jass/ld_block_new_plink/*.ld")
harmonized_GWAS_files=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/harmonized_GWAS_files/*.txt")
harmonized_GWAS_files=Channel.fromPath("/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/last_batch_harmonized/*.txt")
process Impute_GWAS {
publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
memory {8.GB * task.attempt}
time {24.h * task.attempt}
maxRetries = 4
memory {16.GB * task.attempt}
time {72.h * task.attempt}
maxRetries = 6
queue 'dedicated,ggs,common'
input:
file gwas_files from harmonized_GWAS_files
......
GRP1;z_GIANT_HEIGHT z_GIANT_BMI
GRP1;z_IHEC_MPV z_IHEC_EOP
filename Consortium Outcome FullName internalDataLink Type Reference ReferenceLink dataLink Nsample Ncase Ncontrol Nsnp snpid POS CHR a1 a2 freq pval n z OR se index_type imp ncas ncont
MPV.txt IHEC MPV Mean platelet volume Cellular Astle et al. 2016 https://www.ncbi.nlm.nih.gov/pubmed/27863252 http://www.bloodcellgenetics.org 173480 29519497 variant_id effect_allele other_allele effect_allele_frequency p_value beta standard_error rs-number
EOP.txt IHEC EOP Eosinophil percentage of white cells Cellular Astle et al. 2016 https://www.ncbi.nlm.nih.gov/pubmed/27863252 http://www.bloodcellgenetics.org 173480 29483746 variant_id effect_allele other_allele effect_allele_frequency p_value beta standard_error rs-number
......@@ -2,9 +2,9 @@ params.compute_project=false
params.compute_LDSC_matrix=true
params.compute_imputation=true
params.meta_data = "${baseDir}"+"/input_files/meta_data_30_09_2020_format.csv"
params.gwas_folder = '/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/RAW_GWAS'
params.ref_panel = '/pasteur/zeus/projets/p02/GGS_JASS/1._DATA/ImpG_refpanel/'
params.meta_data = "${baseDir}"+"/input_files/test_16_11_2021_format.csv"
params.gwas_folder = '/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/test_data/'
params.ref_panel = '/pasteur/zeus/projets/p02/GGS_JASS/jass_analysis_pipeline/Ref_panel_by_chr/'
params.group = "${baseDir}/input_files/group.txt"
group = file(params.group)
......@@ -31,8 +31,7 @@ parse_correlation_channel = Channel.fromPath("${baseDir}/parse_correlation_resul
process Compute_MAF{
time '1h'
queue 'dedicated,common,ggs'
input:
file ref_panel from ref_chr_channel3.collect()
val chr from chr_channel
......@@ -53,8 +52,7 @@ process Compute_MAF{
process create_WG_reference_panel{
publishDir "${baseDir}/Ref_Panel", pattern: "*.csv", mode: 'copy'
time '1h'
queue 'dedicated,common,ggs'
input:
file maf_files from MAF_channel.collect()
file chr_files from ref_chr_channel.collect()
......@@ -88,8 +86,7 @@ process create_WG_reference_panel{
process meta_data_GWAS{
time '1h'
queue 'dedicated,common,ggs'
output:
file "meta_data_chk*" into meta_data mode flatten
"""
......@@ -108,8 +105,7 @@ process Clean_GWAS {
publishDir "${params.output_folder}/harmonized_GWAS_files/", pattern: "*.txt", mode: 'copy'
publishDir "${params.output_folder}", pattern: "harmonized_GWAS_1_file/*.txt", mode: 'copy'
time '1h'
queue 'dedicated,common,ggs'
input:
file ref_panel from ref_panel_wg_channel
file meta_chunk from meta_data
......@@ -140,10 +136,7 @@ process Clean_GWAS {
process Impute_GWAS {
publishDir "${params.output_folder}", pattern: "imputed_GWAS/*.txt", mode: 'copy'
memory {8.GB * task.attempt}
time {24.h * task.attempt}
maxRetries = 4
queue 'dedicated,ggs,common'
input:
file gwas_files from cleaned_gwas_chr_channel
file ref_file from ref_chr_channel2.collect()
......@@ -195,7 +188,7 @@ process Do_not_Impute_GWAS {
*/
process Munge_LDSC_data {
publishDir "${params.output_folder}", pattern: "ldsc_data/data_*.sumstats.gz", mode: 'copy'
publishDir "${params.output_folder}", pattern: "ldsc_data/data_*.log", mode: 'copy'
publishDir "${params.output_folder}", pattern: "ldsc_data/*.log", mode: 'copy'
time = {1.h * task.attempt}
maxRetries = 4
queue 'dedicated,common,ggs'
......@@ -368,7 +361,6 @@ process get_pheno_group {
}
process Create_project_data {
publishDir "${baseDir}/worktable/", pattern:"worktable_*.hdf5", mode: 'move'
publishDir "${baseDir}/quadrant/", pattern:"quadrant_*.png", mode: 'move'
publishDir "${baseDir}/manhattan/", pattern:"manhattan_*.png", mode: 'move'
......
......@@ -27,32 +27,44 @@ process{
maxRetries=4
maxForks=400
queueSize = 500
errorStrategy='retry'
errorStrategy='ignore'
cache='deep'
withName: 'Compute_MAF' {
container='plink_1.90b5--heea4ae3_0.sif'
time='1h'
queue='dedicated,common,ggs'
cpus=1
}
withName: 'create_WG_reference_panel' {
container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
time='1h'
queue='dedicated,common,ggs'
cpus=1
}
withName: 'meta_data_GWAS' {
time='1h'
queue='dedicated,common,ggs'
cpus=1
}
withName: 'Clean_GWAS' {
memory = '16G'
time='1h'
queue='dedicated,common,ggs'
cpus=1
container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
}
withName: 'Impute_GWAS' {
memory = '8G'
container='raiss_3.1--pyhdfd78af_0.sif'
memory={8.GB * task.attempt}
time={24.h * task.attempt}
maxRetries=4
queue='dedicated,ggs,common'
cpus=1
}
......@@ -62,7 +74,7 @@ process{
}
withName: 'Generate_trait_pair' {
container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
cpus=1
}
......@@ -72,7 +84,7 @@ process{
}
withName: 'Correlation_matrices' {
container='jass_preprocessing_2.1--pyhdfd78af_0.sif'
container='jass_preprocessing_2.2--pyhdfd78af_0.sif'
cpus=1
}
......
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