adjust logging directory

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}; \

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}; \

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}; \