add "docker" AND "singularity" properties in module configs; config.py reads...

add "docker" AND  "singularity" properties in module configs; config.py reads named options correctly

psot/config.py

@@ -64,6 +64,13 @@ class Repository:
                   module['analysis']['parameters'] = {}
               if module['converter']['parameters'] is None:
                   module['converter']['parameters'] = {}
+              if not 'container' in module['analysis'] or module['analysis']['container'] is None:
+                  module['analysis']['container'] = {"docker":None, "singularity":None}
+              elif not 'docker' in module['analysis']['container']:
+                  module['analysis']['container']['docker'] = None
+              elif not 'singularity' in module['analysis']['container']:
+                  module['analysis']['container']['singularity'] = None
+                      
               module['analysis']['script'] = os.path.abspath(os.path.join(self.get_scripts_location(), module['analysis']['script']))
               module['converter']['script'] = os.path.abspath(os.path.join(self.get_scripts_location(), module['converter']['script']))
       return modules

psot/default_repo/modules/blast_vs_swissprot.yaml

@@ -14,7 +14,7 @@ analysis:
         database: '/vol/biodb/uniprot/uniprot_sprot.fasta'
         evalue: 1e-10
         use_accession:
-    container: 'blastp_swissprot'
+    container:
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/modules/ghostx_vs_swissprot.yaml

@@ -12,7 +12,7 @@ analysis:
     script: 'run_ghostx.py'
     parameters:
         database: '/vol/biodb/ghostx/uniprot_sprot'
-    container: 'ghostx_swissprot'
+    container:
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/modules/hmmer_vs_PFAM-A.yaml

@@ -16,7 +16,7 @@ analysis:
     execution:
         cluster:
             chunksize: 200
-    container: 'hmmer_pfam_a'
+    container:
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/modules/signalp.yaml

@@ -14,7 +14,9 @@ analysis:
     # specify additional default configuration here
     parameters:
     # run script in a container
-    container: 'psot'
+    container: 
+        docker: 'cbs-tools'
+        singularity: '/home/ubuntu/project/work/singularity/cbs-tools/cbs-tools.sif'
 
 # The configuration of the script for the json conversion step. 
 converter:

psot/default_repo/modules/targetp.yaml

@@ -14,7 +14,9 @@ analysis:
     # specify additional default configuration here
     parameters:
     # run script in a container
-    container: 'psot'
+    container:
+        docker: 'cbs-tools'
+        singularity: '/home/ubuntu/project/work/singularity/cbs-tools/cbs-tools.sif'
 
 # The configuration of the script for the json conversion step. 
 converter:

psot/default_repo/modules/tmhmm.yaml

@@ -14,7 +14,9 @@ analysis:
     # specify additional default configuration here
     parameters:
     # run script in a container
-    container: 'psot'
+    container:
+        docker: 'cbs-tools'
+        singularity: '/home/ubuntu/project/work/singularity/cbs-tools/cbs-tools.sif'
 
 # The configuration of the script for the json conversion step.
 converter:

psot/default_repo/profiles/custom3.yaml

@@ -6,6 +6,5 @@ modules:
   signalp:
       organism: 'euk'
   tmhmm:
-  hmmer_pfam_a:
   
 

psot/nextflow.py

@@ -256,8 +256,10 @@ def generate_nextflow_config(execution):
         config = {}
         config['id'] = m['id']
         
-        if execution['docker'] or execution['singularity'] and 'container' in m['analysis']:
-            config['container'] = "container = " + "'" + m['analysis']['container'] + "'"
+        if execution['docker'] and m['analysis']['container']['docker']:
+            config['container'] = "container = " + "'" + m['analysis']['container']['docker'] + "'"
+        elif execution['singularity'] and m['analysis']['container']['singularity']:
+            config['container'] = "container = " + "'" + m['analysis']['container']['singularity'] + "'"       
         else:
             config['container'] = ''