config/import clean-up: analysis

2019_GDB/rules/ANALYSIS_RULES

@@ -9,17 +9,13 @@
 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"]
+BARCODES=config["barcodes"]
+ASSEMBLERS = config["assemblers"]
+MAPPERS=["bwa", "mmi"]
+# SAMPLES=config["samples"]
 SAMPLES=["ONT3_MG_xx_Rashi_S11"]
-# BINNING_SAMPLES=config["binning_samples"]
-# HYBRID_ASSEMBLER=config["hybrid_assembler"]
+BINNING_SAMPLES=config["binning_samples"]
+HYBRID_ASSEMBLER=config["hybrid_assembler"]
 
 
 ############################################

2019_GDB/workflows/analysis.smk

 # For running the ANALYSIS "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/ANALYSIS_RULES'