diff --git a/2019_GDB/rules/TAXONOMY_RULES b/2019_GDB/rules/TAXONOMY_RULES
index bdc76d9ea6e1a0525b9cc1f371079a86246c51c0..a10e690b81ec8c02f0d893276200cd2e65a710ca 100755
--- a/2019_GDB/rules/TAXONOMY_RULES
+++ b/2019_GDB/rules/TAXONOMY_RULES
@@ -1,21 +1,5 @@
 # For running the contamination check and taxonomy on the generated MAGs
 
-import os
-from tempfile import TemporaryDirectory
-
-configfile: "config/CONFIG.yaml"
-DATA_DIR = config["data_dir"]
-RESULTS_DIR = config["results_dir"]
-DB_DIR=config["db_dir"]
-BARCODES=config["barcodes"]
-ASSEMBLERS=config["assemblers"]
-MAPPERS=["bwa", "mmi"]
-#SAMPLES=config["samples"]
-SAMPLES=["flye", "megahit", "metaspades_hybrid"]
-BINNING_SAMPLES=config["binning_samples"]
-HYBRID_ASSEMBLER=config["hybrid_assembler"]
-
-
 #####################################
 ######## GTDBTK & CHECKM ############
 #####################################
diff --git a/2019_GDB/workflows/taxonomy.smk b/2019_GDB/workflows/taxonomy.smk
index 733d1ef2433b6e555a7cb4caca5268884339ca7a..2b70c62a9b6d00ebd9ea11f0592db386c7c428e6 100755
--- a/2019_GDB/workflows/taxonomy.smk
+++ b/2019_GDB/workflows/taxonomy.smk
@@ -1,20 +1,6 @@
 # For running the TAXONOMY "workflow"
 
-import os
-from tempfile import TemporaryDirectory
-
-configfile: "config/CONFIG.yaml"
-DATA_DIR = config["data_dir"]
-RESULTS_DIR = config["results_dir"]
-DB_DIR=config["db_dir"]
-BARCODES=config["barcodes"]
-ASSEMBLERS=config["assemblers"]
-MAPPERS=["bwa", "mmi"]
-#SAMPLES=config["samples"]
-SAMPLES=["flye", "megahit", "metaspades_hybrid"]
 BINNING_SAMPLES=config["binning_samples"]
-HYBRID_ASSEMBLER=config["hybrid_assembler"]
-
 
 # specify which rules to run
 include: