Add PlasFlow and RGI

merge checkpoint_snakefile_VG into checkpoint_snakefile to include PlasFlow and RGI

Note: The config file and main snakemake file have been adjusted. Further changes should be made in other snakemake files as only the files for the analysis step have been adjusted.

See commits mentioned in the issue #28 (closed) and #29 (closed).

2019_GDB/rules/checkpoint_ASSEMBLY_ANNOTATION_RULES

 # For running the ASSEMBLY and ANNOTATION workflow for ONT data
 
-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"]
-RUNS=[config["runs"]["first"],
-    config["runs"]["second"]]
-#    config["runs"]["third"]]
-BARCODES=config["barcodes"]
-SAMPLES=["ONT3_MG_xx_Rashi_S11"]
-sr_sample=["ONT3_MG_xx_Rashi_S11"]
-# SAMPLES_ALL=config["samples"]
-REFERENCES=["igc", "hg38"]
+RUNS=[
+    config["runs"]["first"],
+    config["runs"]["second"],
+#    config["runs"]["third"]
+]
 IGC_URI=config["igc"]["uri"]
 HG38_URI=config["hg38"]["uri"]
-ASSEMBLERS=config["assemblers"]
-MAPPERS=["bwa_mem", "minimap2"]
-
 
 ######
 # RULES