config/import clean-up: metaT

2019_GDB/rules/METAT_RULES

 # Rules for mapping the metaT reads to the different assemblies
 
-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"]
-ASSEMBLERS=config["assemblers"]
-MAPPERS=["bwa", "mmi"]
-# SAMPLES=config["samples"]
-SAMPLES=["flye", "megathit", "metaspades_hybrid"]
-BINNING_SAMPLES=config["binning_samples"]
-HYBRID_ASSEMBLER=config["hybrid_assembler"]
-
-
 ###########
 ## metaT ##
 ###########

2019_GDB/workflows/metat.smk

 # Workflow for running mapping metaT reads to different assemblies using different mappers for the Binning 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:
     '../rules/METAT_RULES'