diff --git a/modules/sanity_checks.nf b/modules/sanity_checks.nf index d6eb9fc257b439083e726f2e0c032b7771d658ac..925416c13527fe38379239883a87fe00c6b6986c 100755 --- a/modules/sanity_checks.nf +++ b/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} """ }