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/config/CONFIG.yaml

-# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
-# steps: "binning taxonomy analysis"
-steps: "analysis"
+steps: ["assembly_annotation", "mapping", "metaT", "mmseq", "binning", "taxonomy", "analysis"]
+
 # analysis_steps: ["cdhit", "mappability", "crispr", "plasmids", "amr"]
-analysis_steps: ["plasmids", "amr"]
+analysis_steps: ["cdhit", "mappability", "crispr", "plasmids", "amr"]
+
 # working directory containing all relevant data,
 # i.e. prefix for data, results, DBs etc.
 work_dir: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB"
 data_dir: "data"
 results_dir: "results"
 db_dir: "dbs"
+
 runs:
     first: "S1_SizeSelected"
     second: "S3_Gtube"
 #    third: "20181108_0827_test"
+
 # assemblers: ["flye"]
 assemblers: ["flye", "megahit", "metaspades", "metaspades_hybrid"]
+
 p7zip:
     bin: "/home/users/claczny/apps/software/p7zip_16.02/bin/7za"
     threads: 4
@@ -25,8 +28,10 @@ ont_fast5_api:
         threads: 8
 flowcell: "FLO-MIN106"
 kit: "SQK-LSK109"
+
 #barcodes: ["barcode06", "barcode07", "barcode08", "barcode09", "barcode10"]
 barcodes: ["no_barcode"]
+
 guppy_cpu:
     path: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin"
     bin: "/scratch/users/claczny/ont/apps/software/ont-guppy-cpu-3.1.5_linux64/bin/guppy_basecaller"
@@ -52,10 +57,13 @@ guppy_barcoder:
     version: "3.4.5+fb1fbfb"
     records_per_fastq: 8000
     threads: 8
+
 nanostats:
+
 short_reads_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/raw/short_reads"
 #short_reads_prefix: "/mnt/isilon/projects/lcsb_sequencing/transfer/bioecosystem/Rashi/2019/Apr/fastq"
 metaT_prefix: "/scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/data/metaT"
+
 fastp:
     min_length: 40
 minimap2:
@@ -104,10 +112,9 @@ metaspades:
     threads: 28
 mmseq2:
     threads: 24
+
 # Define sample names
-#samples: ["flye", "megahit", "metaspades_hybrid"]
-# samples: ["flye", "megahit"]
-# samples: ["metaspades_hybrid"]
+samples: ["ONT3_MG_xx_Rashi_S11"]
 binning_samples: ["flye", "megahit", "bwa_sr_metaspades_hybrid", "bwa_lr_metaspades_hybrid", "bwa_merged_metaspades_hybrid", "mmi_sr_metaspades_hybrid", "mmi_lr_metaspades_hybrid", "mmi_merged_metaspades_hybrid"]
 
 # Hybrid assembler
@@ -127,10 +134,11 @@ kraken2_database: "/scratch/users/bkunath/Kraken2/maxikraken2_1903_140GB/"
 
 # Path to DAS_Tool
 DAS_Tool:
-        path: "/home/users/sbusi/apps/DAS_Tool-master"
-        bin: "/home/users/sbusi/apps/DAS_Tool-master/src/"
+    path: "/home/users/sbusi/apps/DAS_Tool-master"
+    bin: "/home/users/sbusi/apps/DAS_Tool-master/src/"
 
 # Path to DAS_Tool database
+# TODO: mv to DAS_Tool
 dastool_database: "/home/users/sbusi/apps/DAS_Tool-master/db/"
 
 # Mapping options
@@ -152,13 +160,15 @@ GTDBTK:
     DATA: "/home/users/sbusi/apps/db/gtdbtk/release89"
 
 # Rscript path
+# TODO: mv to DAS_Tool
 Rscript: "/home/users/sbusi/apps/miniconda3/envs/dastool/bin/"
 
+# XXX
 mmseqs:
-     path: "/home/users/sbusi/apps/mmseqs/bin"
-     createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
-     rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
-     convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
+    path: "/home/users/sbusi/apps/mmseqs/bin"
+    createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
+    rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
+    convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
 
 # CRISPR
 CASC: