database directory is written automatically in nextflow config (docker or singularity scope)

psot/config.py

@@ -11,7 +11,7 @@ class Repository:
   def load_config(self):
       '''return a dictionary with the whole configuration for this repository'''
       config = self.load_config_file()
-      config['profiles'] = self.load_profiles(config)
+      config['profiles'] = self.load_profiles()
       config['modules'] = self.load_modules(config)
       self.normalize_profiles(config['profiles'])
       return config
@@ -41,7 +41,7 @@ class Repository:
             config = yaml.load(f)
       return config
 
-  def load_profiles(self, config):
+  def load_profiles(self):
       profiles = []
       for manifest in self.get_profile_manifests():
           with (open(manifest)) as f:

psot/main.py

@@ -73,6 +73,7 @@ def generate_execution(config, args):
     execution['output'] = os.path.abspath(args.output)
     execution['install_path'] = config['install_path']
     execution['helpers_path'] = config['helpers_path']
+    execution['database_path'] = config['databases']['localpath']
     execution['docker'] = args.docker
     execution['singularity'] = args.singularity
     if 'venv' in config:

psot/nextflow.py

@@ -337,6 +337,7 @@ def generate_nextflow_script(execution):
 
 def generate_nextflow_config(execution):
     modules = execution['modules']
+    database_path = execution['database_path']
     
     fragments = []
     
@@ -344,15 +345,15 @@ def generate_nextflow_config(execution):
         fragments.append('''docker {
             enabled = 'true'
             fixOwnership = 'true'
-            runOptions = '--volume=/home/ubuntu/db:/databases'
+            runOptions = '--volume={path}/databases'
         }
-        ''')
+        '''.format(path=database_path))
     elif execution['singularity']:
         fragments.append('''singularity {
             enabled = 'true'
-            runOptions = '--bind /home/ubuntu/db:/databases'
+            runOptions = '--bind {path}:/databases'
         }
-        ''')
+        '''.format(path=database_path))
         
     fragments.append('''process { ''')