sole issue with reading paths for RAW_DIR and OUT_DIR in configuration file....

sole issue with reading paths for RAW_DIR and OUT_DIR in configuration file. Avoids using PWD and asks for always providing absolute paths

Snakefile

@@ -68,22 +68,47 @@ except:
         configfile: configfile_path
         print("... Configuration file: {}".format(configfile_path), file=sys.stderr)
 finally:
-    print("Configuration of MetaSnk:", file=sys.stderr)
+    print("Provided configuration for 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
 ##----------------------------------------------------------------------------##
-PWD = os.environ["PWD"]
-RAW_FASTQ_DIR = eval(config['RAW_DIR'])
-OUT_DIR = eval(config['OUT_DIR'])
+print("MetaSnk is setting local variables ...")
+
+try:
+    print("Setting RAW_DIR")
+    if os.path.exists(config['RAW_DIR'])==False:
+        raise FileNotFoundError
+    else:
+        RAW_FASTQ_DIR = config['RAW_DIR']
+        print("RAW_DIR: {}".format(RAW_FASTQ_DIR), file=sys.stderr)
+except FileNotFoundError:
+    print("  Provided path does not exist!\n"+\
+          "  Please provide an absolute path for RAW_DIR in your configuration file!")
+    exit(1)
+
+try:
+    print("Setting OUT_DIR")
+    if os.path.exists(config['OUT_DIR'])==False:
+        raise FileNotFoundError
+    else:
+        OUT_DIR = config['OUT_DIR']
+        print("OUT_DIR: {}".format(OUT_DIR), file=sys.stderr)
+except FileNotFoundError:
+    print("  Provided path does not exist!\n"+\
+          "  Please provide absolute path for OUT_DIR in your configuration file!")
+    exit(1)
+OUT_DIR = 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'
 PREQC_SIF = METASNK_DB_DIR+'/singularity/MetagenomicSnake_preqc_v0_1.sif'
 METAPROF_SIF = METASNK_DB_DIR+'/singularity/OmicSingularities_metaprof.sif'
-HUMAN_REF = eval(config['preprocess']['filter_human']['bbmap_reference'])
 
+HUMAN_REF = eval(config['preprocess']['filter_human']['bbmap_reference'])
+print("HUMAN_REF: {}".format(HUMAN_REF), file=sys.stderr)
 ##----------------------------------------------------------------------------##
 ## Fastq files to be processed
 ##----------------------------------------------------------------------------##

config.yaml

@@ -10,10 +10,21 @@
 #   or a comma-delimited string of bind path specifications can be used.
 #
 
-# Absolute PATH to folder where to find fastq files
-RAW_DIR: "PWD+'/data/raw'"
-# Absolute PATH to folder where to place output files
-OUT_DIR: "PWD+'/data/interim/MetaSnk'"
+# Always provide an ABSOLUTE PATH to the folder where to find fastq files
+# MetaSnk expects to find the raw fastq files in a directory where 
+# they are grouped into datasets (one or multiple).
+# Inside the RAW_DIR folder, each dataset directory (named at the user's discretion) 
+# must contain a directory named 'fastq', where fastq files are placed, 
+# accompanied by a sample_metatada.tsv file:
+# $RAW_DIR
+# ├── dataset_test_1
+#    ├── fastq
+#    |     ├── sampleID-RUN_LANE-R1.fastq.gz
+#    |     ├── sampleID-RUN_LANE-R2.fastq.gz
+#    └── sample_metadata.tsv
+RAW_DIR: ''
+# Always provide ABSOLUTE PATH to folder where to place output files
+OUT_DIR: ''
 
 #
 SAMPLE_UNITS: