rm datadir parameter

Snakefile

@@ -41,7 +41,6 @@ if os.path.exists(CUSTOM_CONFIG_PATH):
 SRCDIR = os.environ.get("SRCDIR", config['imp_src'])
 
 # get parameters from the command line
-DATADIR = os.environ.get("DATADIR", config['datadir'])
 OUTPUTDIR = os.environ.get("OUTPUTDIR", config['outputdir'])
 MG = os.environ.get("MG", config['raws']['Metagenomics']).split()
 MT = os.environ.get("MT", config['raws']['Metatranscriptomics']).split()

rules/Preprocessing/MG.rules

@@ -2,7 +2,7 @@ rule PREPROCESSING_MG_GET_FILES:
     message:
         "Preparing MG DATA files : %s." % ', '.join(MG)
     input:
-        expand('{dir}/{raw}', raw=MG, dir=DATADIR)
+        MG
     output:
         expand('{dir}/{raw}', raw=['MG.R1.fq', 'MG.R2.fq'], dir=P_OUT)
     benchmark:

rules/Preprocessing/MT.rules

@@ -2,7 +2,7 @@ rule PREPROCESSING_MT_GET_FILES:
     message:
         "Preparing MT DATA files : %s." % ', '.join(MT)
     input:
-        expand('{dir}/{raw}', raw=MT, dir=DATADIR)
+        MT
     output:
         expand('{dir}/{raw}', raw=['MT.R1.fq', 'MT.R2.fq'], dir=P_OUT)
     run: