sanity_check_module

modules/sanity_checks.nf

@@ -3,7 +3,7 @@
 
 params.output_folder = "/pasteur/zeus/projets/p02/GGS_JASS/DATA_BATCH_04_11_2022/"
 params.ancestry = ""
-
+params.harmonized_files = ""
 
 process Sanity_checks {
     publishDir "${params.output_folder}", pattern: "sanity_checks/*.txt", mode: 'copy'
@@ -17,6 +17,6 @@ process Sanity_checks {
     echo \$trait
     ls
     mkdir -p sanity_checks_${params.EUR}
-    raiss sanity-check --trait \${trait} --harmonized-folder ${param} --imputed-folder /pasteur/zeus/projets/p02/GGS_JASS/DATA_BATCH_04_11_2022/imputed_gnomad/ --output-path ./sanity_checks/sanity_report_${params.EUR}
+    raiss sanity-check --trait \${trait} --harmonized-folder ${params.harmonized_files} --imputed-folder ${params.imputed_files} --output-path ./sanity_checks/sanity_report_${params.ancestry}
     """
   }