Commit f80d131c authored by hjulienne's avatar hjulienne

created placeholder

parent 34322b1b
......@@ -11,12 +11,13 @@ The current pipeline integrate the following workflow:
The following Item are necessary to run JASS pipeline
1. A meta-data file describing GWAS (see example file in ./input_files/test1.csv)
2. A path toward a folder containing the summary statistics to analyze
1. --input_folder : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv)
2. --gwas_folder : A path toward a folder containing the summary statistics to analyze
3. A folder containing a Reference Panel in the .bim, .bed, .fam format
4. A path toward a folder to write pipeline results (inittable, worktable...)
5. If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line
4. If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line
## Optional parameters
. A path toward a folder to write pipeline results (inittable, worktable...). by default results will be publish in the workflow directory.
## Usage of nextflow pipeline
......
......@@ -7,23 +7,23 @@ params.compute_imputation=false
params.meta_data = "test_final.csv"
params.input_folder = ${baseDir}+"/input_files/"
params.GWAS_path = "/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/"
params.gwas_folder = "/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/"
params.group = params.input_folder+"/group.txt"
group = file(params.group)
params.region = params.input_folder+"fourier_ls-all.bed"
output_folder = "/pasteur/projets/policy01/PCMA/JASS_pipeline_output/"
params.output_folder = $baseDir
GWAS_labels = params.input_folder + params.input_folder
Region_channel = Channel.fromPath(params.region)
Region_channel2 = Channel.fromPath(params.region)
diagnostic_folder= output_folder + "/sample_size/"
harmonized_GWAS_folder = output_folder + "harmonized_GWAS/"
harmonized_GWAS_1_file_folder = output_folder + "harmonized_GWAS/"
diagnostic_folder= params.output_folder + "/sample_size/"
harmonized_GWAS_folder = params.output_folder + "harmonized_GWAS_by_chr/"
harmonized_GWAS_1_file_folder = params.output_folder + "harmonized_GWAS_WG/"
chr_channel = Channel.from(1..22)
......@@ -40,33 +40,6 @@ parse_correlation_channel = Channel.fromPath('${baseDir}/parse_correlation_resul
process prepare_output_folder{
input:
file ref_panel from ref_chr_channel3.collect()
val chr from chr_channel
output:
file "*.frq" into MAF_channel
"""
if [ ! -d ${diagnostic_folder} ]
then
mkdir ${diagnostic_folder}
fi
if [ ! -d ${harmonized_GWAS_folder} ]
then
mkdir ${harmonized_GWAS_folder}
fi
if [ ! -d ${harmonized_GWAS_1_file_folder} ]
then
mkdir ${harmonized_GWAS_1_file_folder}
fi
"""
}
process Compute_MAF{
input:
file ref_panel from ref_chr_channel3.collect()
......@@ -150,7 +123,7 @@ process Clean_GWAS {
"""
mkdir harmonized_GWAS_1_file
echo ${params.GWAS_path}
echo ${params.gwas_folder}
working_dir=\$(pwd)
echo \$working_dir
full_path=\$working_dir/${meta_chunk}
......@@ -158,7 +131,7 @@ process Clean_GWAS {
echo \$full_path
jass_preprocessing --gwas-info \$full_path --ref-path ${ref_panel} \
--input-folder ${params.GWAS_path} --diagnostic-folder ${diagnostic_folder} \
--input-folder ${params.gwas_folder} --diagnostic-folder ${diagnostic_folder} \
--output-folder ./ --output-folder-1-file harmonized_GWAS_1_file/
"""
......@@ -171,7 +144,7 @@ process Impute_GWAS {
time '8h'
input:
file gwas_files from cleaned_gwas_chr_channel
start = timeit.timeit() file ref_file from ref_chr_channel2.collect()
file ref_file from ref_chr_channel2.collect()
file ld_file from ld_channel.collect()
output:
file "imputed_GWAS/*.txt" into imputed_gwas_channel
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment