From 3b6ed7edfa5104f829428e6af59ad64e5d9e2c25 Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Wed, 3 Jun 2020 13:39:37 +0200
Subject: [PATCH] config/import clean-up: binning

---
 2019_GDB/rules/BINNING_RULES   | 24 ++++++++++++------------
 2019_GDB/workflows/binning.smk | 22 +++++++++++-----------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/2019_GDB/rules/BINNING_RULES b/2019_GDB/rules/BINNING_RULES
index 0b38b5c..5f06fb9 100755
--- a/2019_GDB/rules/BINNING_RULES
+++ b/2019_GDB/rules/BINNING_RULES
@@ -1,19 +1,19 @@
 # Rules for BINNING workflow, i.e. generating MAGs from assemblies
 
-import os
-from tempfile import TemporaryDirectory
+# 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"]
+# 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"]
+# SAMPLES=["flye", "megahit", "metaspades_hybrid"]
+# BINNING_SAMPLES=config["binning_samples"]
+# HYBRID_ASSEMBLER=config["hybrid_assembler"]
 
 
 ###################
diff --git a/2019_GDB/workflows/binning.smk b/2019_GDB/workflows/binning.smk
index d945422..261dd73 100755
--- a/2019_GDB/workflows/binning.smk
+++ b/2019_GDB/workflows/binning.smk
@@ -1,19 +1,19 @@
 # For running the BINNING "workflow"
 
-import os
-from tempfile import TemporaryDirectory
+# 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"]
+# 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"]
+# SAMPLES=["flye", "megahit", "metaspades_hybrid"]
 BINNING_SAMPLES=config["binning_samples"]
-HYBRID_ASSEMBLER=config["hybrid_assembler"]
+# HYBRID_ASSEMBLER=config["hybrid_assembler"]
 
 
 # specify which rules to run
-- 
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