Commit abf7b225 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

add to readme fiw publication folder

parent 16830b02
......@@ -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
......@@ -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
......
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