readme writing

README.md

 # JASS analysis pipeline
+## Overview
 
 We present here a nextflow pipeline to harmonize, impute and analyze jointly GWAS summary statistics.
 
 The current pipeline integrate the following workflow:
 
+![workflow image](./doc/workflow.png=650x570)
 
+## Required Input
 
-![workflow image](./doc/workflow.png)
+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
+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
+
+
+## Usage of nextflow pipeline
+
+Install nextflow as explain here : https://www.nextflow.io/docs/latest/getstarted.html
+
+
+Clone the current repository locally:
+
+```
+    git clone https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline.git
+```
+
+Once done you can launch the pipeline as:

jass_pipeline.nf

+
 params.compute_project=false
 params.compute_LDSC_matrix=true
 params.compute_imputation=false
 
-params.group = "$baseDir/input_files/group.txt"
+
+params.meta_data = "test_final.csv"
+
+params.input_folder = ${baseDir}+"/input_files/"
+params.GWAS_path = "/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/"
+
+
+params.group = params.input_folder+"/group.txt"
 group = file(params.group)
-netPath = "/pasteur/projets/policy01/PCMA/"
 
+params.region = params.input_folder+"fourier_ls-all.bed"
 output_folder = "/pasteur/projets/policy01/PCMA/JASS_pipeline_output/"
 
-GWAS_labels = netPath + 'jass_analysis_pipeline/input_files/test_final.csv'
-GWAS_path = "/pasteur/projets/policy01/PCMA/1._DATA/RAW.GWAS/"
+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/"
 
 chr_channel = Channel.from(1..22)
+
 ref_chr_channel=Channel.fromPath("/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel/chr*.eur.1pct.bim")
 ref_chr_channel2=Channel.fromPath("/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel/chr*.eur.1pct.bim")
 ref_chr_channel3=Channel.fromPath("/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel/chr*.eur.1pct.*")
 
 ld_channel=Channel.fromPath("/pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/ld_block_new_plink/*.ld")
 
-Region_channel = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/input_files/fourier_ls-all.bed')
-Region_channel2 = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/input_files/fourier_ls-all.bed')
+/* Script channels*/
+extract_sample_size_script_channel = Channel.fromPath('${baseDir}/extract_sample_size.py')
+generate_trait_pairs_channel = Channel.fromPath('${baseDir}/generate_trait_pairs.py')
+parse_correlation_channel = Channel.fromPath('${baseDir}/parse_correlation_results.py')
+
+
+
+
+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
+
+    """
+}
 
-extract_sample_size_script_channel = Channel.fromPath('/pasteur/projets/policy01/PCMA/jass_analysis_pipeline/extract_sample_size.py')
 
 process Compute_MAF{
     input:
@@ -110,7 +150,7 @@ process Clean_GWAS {
     """
     mkdir harmonized_GWAS_1_file
 
-    echo ${GWAS_path}
+    echo ${params.GWAS_path}
     working_dir=\$(pwd)
     echo \$working_dir
     full_path=\$working_dir/${meta_chunk}
@@ -118,7 +158,7 @@ process Clean_GWAS {
     echo \$full_path
 
     jass_preprocessing --gwas-info \$full_path --ref-path ${ref_panel} \
-        --input-folder ${GWAS_path} --diagnostic-folder ${diagnostic_folder} \
+        --input-folder ${params.GWAS_path} --diagnostic-folder ${diagnostic_folder} \
         --output-folder ./ --output-folder-1-file harmonized_GWAS_1_file/
 
     """
@@ -131,7 +171,7 @@ process Impute_GWAS {
     time '8h'
     input:
         file gwas_files from cleaned_gwas_chr_channel
-        file ref_file from ref_chr_channel2.collect()
+        start = timeit.timeit()    file ref_file from ref_chr_channel2.collect()
         file ld_file from ld_channel.collect()
     output:
         file "imputed_GWAS/*.txt" into imputed_gwas_channel
@@ -210,13 +250,14 @@ process Munge_LDSC_data {
 process Generate_trait_pair {
 
     input:
+        file generate_trait_pairs_script from generate_trait_pairs_channel
         file ldsc_data from ldsc_data_channel.collect()
     output:
         file "pairs_chunk_*.txt" into combi_channel mode flatten
     when:
         params.compute_LDSC_matrix
     """
-    python3 ${baseDir}/generate_trait_pairs.py
+    python3 ${generate_trait_pairs_script}
     """
 }
 
@@ -255,13 +296,14 @@ process Correlation_matrices {
     //publishDir "${baseDir}/Correlation_matrices/", pattern: "*.csv", mode: 'copy'
 
     input:
+        file parsing_script from parse_correlation_channel
         file ldsc_data from cor_log_channel.collect()
     output:
         file "Covariance_matrix_H0.csv" into cov_H0_matrice_channel
     when:
         params.compute_LDSC_matrix
     """
-    python3 ${baseDir}/parse_correlation_results.py
+    python3 ${parsing_script}
 
     """
 }

nextflow.config

@@ -36,7 +36,7 @@ process{
 
 //docker://quay.io/biocontainers/jass_preprocessing:1.0--py_0
     withName: 'create_WG_reference_panel' {
-		container='jass_preprocessing_1.0--py_0.sif'
+		container='jass_preprocessing_2.0--py_0.sif'
 		cpus=1
 	}
 
@@ -45,7 +45,7 @@ process{
     }
 
     withName: 'Clean_GWAS' {
-      //container='jass_preprocessing_1.0--py_0.sif'
+//      container='jass_preprocessing_2.0--py_0.sif'
         cpus=1
     }
 
@@ -60,7 +60,7 @@ process{
     }
 
     withName: 'Generate_trait_pair' {
-    container='jass_preprocessing_1.0--py_0.sif'
+    container='jass_preprocessing_2.0--py_0.sif'
     cpus=1
     }
 
@@ -70,7 +70,7 @@ process{
     }
 
     withName: 'Correlation_matrices' {
-      container='jass_preprocessing_1.0--py_0.sif'
+      container='jass_preprocessing_2.0--py_0.sif'
         cpus=1
     }