diff --git a/.gitignore b/.gitignore
index 64c3f172c3c2dcc090d073e8f27a145b0e291725..1401e74ef0bb8b609b7694f1dfa842c5d205a70d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,15 +3,14 @@
 !workflow/*
 !workflow/Snakefile
 !workflow/
-!scripts
-!scripts/*
-!scripts/
-scripts/.snakemake*
+!workflow/scripts/
+!workflow/scripts/*
+workflow/scripts/.snakemake*
 !config.yaml
 !samples.csv
 !environment.txt
 !LICENSE.md
 !README.md
-!rules
-!rules/*
+!workflow/rules
+!workflow/rules/*
 !.gitignore