From 24a5de557f572f8c045cf3f1b5006cd118f6c8bc Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Fri, 10 Feb 2023 11:46:05 +0100
Subject: [PATCH] sanity_check_module
---
modules/sanity_checks.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/sanity_checks.nf b/modules/sanity_checks.nf
index d6eb9fc..925416c 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}
"""
}
--
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