add to readme fiw publication folder

README.md

@@ -33,9 +33,9 @@ Once done you can launch the pipeline as:
 
 ## Required Input
 
-The following Item are necessary to run JASS pipeline
+The following Item are necessary to run JASS pipeline on real data
 
-1. --meta_data : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv)
+1. --meta_data : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv and [jass_preprocessing documentation](http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/))
 2. --gwas_folder : A path toward a folder containing the summary statistics to analyze
 3. --ref_panel :A folder containing a Reference Panel in the .bim, .bed, .fam format
 4. --ld-folder : A path toward a folder containing LD matrices (that can be generated from the reference panel with the raiss package as described here : http://statistical-genetics.pages.pasteur.fr/raiss/#precomputation-of-ld-correlation)
@@ -46,4 +46,4 @@ The following Item are necessary to run JASS pipeline
 
 * --output_folder : 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
+Parameters can be specified in command line or by editing the

jass_pipeline.nf

@@ -104,7 +104,7 @@ process meta_data_GWAS{
 process Clean_GWAS {
 
     publishDir "${params.output_folder}/harmonized_GWAS_files/", pattern: "*.txt", mode: 'copy'
-    publishDir "${params.output_folder}", pattern: "*.txt", mode: 'copy'
+    publishDir "${params.output_folder}", pattern: "harmonized_GWAS_1_file/*.txt", mode: 'copy'
 
     input:
         file ref_panel from ref_panel_wg_channel