config/import clean-up: taxonomy

2019_GDB/rules/TAXONOMY_RULES

 # 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 ############
 #####################################

2019_GDB/workflows/taxonomy.smk

 # 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: