fixed issue with import of utils

tiagofilipe12 · Sep 7, 2018 · f3e9f2f · f3e9f2f
1 parent 480a341
commit f3e9f2f
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -8,7 +8,7 @@ manifest {
 
 // sets PYTHONPATH for utils to be available for templates
 env {
-    PYTHONPATH = "$baseDir/templates"
+    PYTHONPATH = "$baseDir/templates:$baseDir/templates/assemblerflow_utils:\$PYTHONPATH"
 }
 
 //manifest.mainScript = 'main.nf'

diff --git a/templates/mapping2json.py b/templates/mapping2json.py
@@ -36,7 +36,7 @@
 import os
 import json
 
-from templates.assemblerflow_utils import get_logger, MainWrapper
+from assemblerflow_utils.assemblerflow_base import get_logger, MainWrapper
 
 logger = get_logger(__file__)
 
@@ -66,7 +66,8 @@ def depthfilereader(depth_file, plasmid_length, cutoff):
     cutoff: str
         the cutoff used to trim the unwanted matches for the minimum coverage
         results from mapping. This is then converted into a float within this
-        function in order to compare with the value returned from the perc_value_per_ref.
+        function in order to compare with the value returned from the
+        perc_value_per_ref.
 
     Returns
     -------

diff --git a/templates/mashdist2json.py b/templates/mashdist2json.py
@@ -30,7 +30,7 @@
 import os
 import json
 
-from templates.assemblerflow_utils import get_logger, MainWrapper
+from assemblerflow_utils.assemblerflow_base import get_logger, MainWrapper
 
 logger = get_logger(__file__)
 

diff --git a/templates/mashscreen2json.py b/templates/mashscreen2json.py
@@ -30,7 +30,7 @@
 import os
 import json
 
-from templates.assemblerflow_utils import get_logger, MainWrapper
+from assemblerflow_utils.assemblerflow_base import get_logger, MainWrapper
 
 logger = get_logger(__file__)