diff --git a/Snakefile b/Snakefile
index 647635105669b89270297800c02044b180309a31..acc07ad64bc70ec381bbde952dcb359c3f078ba7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -353,7 +353,7 @@ rule generate_alfa_index:
 	singularity: 
 		"docker://zavolab/alfa:1.1.1"
 	log: 
-		os.path.join(config["local_log"], "{organism}_{index_size}_generate_alfa_index.log")
+		os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
 	shell:
 		"alfa -a {input.gtf} \
 			-g {params.genome_index} \
@@ -416,7 +416,7 @@ rule alfa_bg_all_samples:
 	# singularity:
 	# 	"docker://zavolab/alfa:1.1.1"
 	conda: os.path.abspath("../../envs/env_alfa.yaml")
-	log: os.path.abspath(os.path.join(config["local_log"], "ALFA", "alfa_bg_all_samples.log"))
+	log: os.path.abspath(os.path.join(config["log_dir"], "ALFA", "alfa_bg_all_samples.log"))
 	shell:
 		""" 
 		mkdir -p {params.out_dir}; \
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 1a353fa89b1e9cd1db185fb30d281e8b93e0a67e..f61ee56df9acfb9ce7fd783c3c8967ed3e562933 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -385,7 +385,7 @@ rule star_rpm_paired_end:
 		stranded = "Stranded"
 	singularity:
 		"docker://zavolab/star:2.6.0a"
-	log: os.path.join(config["local_log"], "paired_end", "{sample}", "star_rpm_paired_end.log")
+	log: os.path.join(config["log_dir"], "paired_end", "{sample}", "star_rpm_paired_end.log")
 	threads: 4
 	shell:
 		"""
@@ -446,7 +446,7 @@ rule alfa_bg_paired_end:
 		name = "{sample}"
 	singularity:
 		"docker://zavolab/alfa:1.1.1"
-	log: os.path.abspath(os.path.join(config["local_log"], "paired_end", "{sample}", "alfa_bg_paired_end.log"))
+	log: os.path.abspath(os.path.join(config["log_dir"], "paired_end", "{sample}", "alfa_bg_paired_end.log"))
 	shell:
 		""" 
 		cd {params.out_dir}; \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 8cb818fcdf837f8357d876cab2f7038666fddd36..60e539ea5f4fa9dfdc955200675848d30fd082d0 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -311,7 +311,7 @@ rule star_rpm_single_end:
 		stranded = "Stranded"
 	singularity:
 		"docker://zavolab/star:2.6.0a"
-	log: os.path.join(config["local_log"], "single_end", "{sample}", "star_rpm_single_end.log")
+	log: os.path.join(config["log_dir"], "single_end", "{sample}", "star_rpm_single_end.log")
 	threads: 4
 	shell:
 		"""
@@ -373,7 +373,7 @@ rule alfa_bg_single_end:
 		name = "{sample}"
 	singularity:
 		"docker://zavolab/alfa:1.1.1"
-	log: os.path.abspath(os.path.join(config["local_log"], "single_end", "{sample}", "alfa_bg_single_end.log"))
+	log: os.path.abspath(os.path.join(config["log_dir"], "single_end", "{sample}", "alfa_bg_single_end.log"))
 	shell:
 		""" 
 		cd {params.out_dir}; \