correct bug when setting connfiguration with --configfile at execution, and...

correct bug when setting connfiguration with --configfile at execution, and allow use of environmental variable PWD in config.yaml

Snakefile

@@ -50,8 +50,9 @@ else:
 ## Configuration of MetaSnK
 ##----------------------------------------------------------------------------##
 try:
-    configfile_path = config['configfile_path']
-    print("Configuration file: {}".format(configfile_path), file=sys.stderr)
+    config['RAW_DIR']
+    #configfile_path = config['configfile_path']
+    print("Configuration file provided at execution!", file=sys.stderr)
 except:
     print("Configuration file config.yaml not especified at execution!", file=sys.stderr)
     try:
@@ -66,12 +67,16 @@ except:
         configfile_path = workflow_path + "/config.yaml"
         configfile: configfile_path
         print("... Configuration file: {}".format(configfile_path), file=sys.stderr)
+finally:
+    print("Configuration of MetaSnk:", file=sys.stderr)
+    my_temp=[print("    {}:{}\n".format(key,value), file=sys.stderr) for key,value in config.items()]
 
 ##----------------------------------------------------------------------------##
 ## Define paths and local variables
 ##----------------------------------------------------------------------------##
-RAW_FASTQ_DIR = config['RAW_DIR']
-OUT_DIR = config['OUT_DIR']
+PWD = os.environ["PWD"]
+RAW_FASTQ_DIR = eval(config['RAW_DIR'])
+OUT_DIR = eval(config['OUT_DIR'])
 METASNK_DB_DIR = os.environ["METASNK_DBS"]
 SHUB_PREQC_SIF = 'shub://mticlla/MetagenomicSnake:preqc_v0_1'
 SHUB_METAPROF_SIF = 'shub://mticlla/OmicSingularities:metaprof'

config.yaml

@@ -11,9 +11,9 @@
 #
 
 # Absolute PATH to folder where to find fastq files
-RAW_DIR: '/home/mticlla/Documents/Git_repositories/metagenomicsnake_testdata/data/raw'
+RAW_DIR: "PWD+'/data/raw'"
 # Absolute PATH to folder where to place output files
-OUT_DIR: '/home/mticlla/Documents/Git_repositories/metagenomicsnake_testdata/data/interim/MetaSnk'
+OUT_DIR: "PWD+'/data/interim/MetaSnk'"
 
 #
 SAMPLE_UNITS: