Removed working directory path in .ini file. ariaproject now generated using...

Removed working directory path in .ini file. ariaproject now generated using outdir command line arg

ariaec/conf/aria_ec.ini

@@ -73,7 +73,6 @@ nd_control:                                 0
 runid:                                      1
 cpus:                                       100
 host_command:                               sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
-working_directory:                          data/examples/out/setup
 temp_root:                                  data/examples/out/setup
 parameter_definition:                       automatic
 ss_dist_format:                             tbl

ariaec/econverter.py

@@ -712,6 +712,15 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
     def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files,
                           desc=""):
+        """
+        Generate ariaproject.xml file
+        :param aria_template: ariaproject.xml template path
+        :param seqfile:
+        :param dist_files:
+        :param tbl_files:
+        :param desc:
+        :return:
+        """
         if aria_template:
             template = os.path.abspath(aria_template)
 
@@ -737,26 +746,24 @@ class AriaEcXMLConverter(AriaXMLConverter):
                      'the ratio %.2f:%.2f' % (steps_1, steps_2))
 
         aria_project_dict.update(self.settings.setup.config)
-        work_dir = os.path.abspath(aria_project_dict['working_directory'])
+        work_dir = os.path.abspath(self.settings.outdir)
         temp_root = os.path.abspath(aria_project_dict['temp_root'])
 
         if not os.path.exists(work_dir) or not os.path.exists(temp_root):
-            logger.info("Working dir %s and temp directory %s doesn't exist." % (
-                work_dir, temp_root))
+            logger.info("Working dir %s doesn't exist." % work_dir)
             logger.info("Create new directory %s" % work_dir)
             os.makedirs(work_dir)
+
+        if not os.path.exists(temp_root):
+            logger.info("Temp directory %s doesn't exist." % temp_root)
             logger.info("Create new directory %s" % temp_root)
             os.makedirs(temp_root)
 
-        for direct in (work_dir, temp_root):
-
-            if not os.path.exists(os.path.join(direct, self.outprefix)):
-                os.makedirs(os.path.join(direct, self.outprefix))
-
-            if not os.path.exists(os.path.join(direct, self.outprefix, desc)):
-                os.makedirs(os.path.join(direct, self.outprefix, desc))
+        if not os.path.exists(os.path.join(temp_root, self.outprefix)):
+            os.makedirs(os.path.join(temp_root, self.outprefix))
+        if not os.path.exists(os.path.join(temp_root, self.outprefix, desc)):
+            os.makedirs(os.path.join(temp_root, self.outprefix, desc))
 
-        work_dir = os.path.join(work_dir, self.outprefix, desc)
         temp_root = os.path.join(temp_root, self.outprefix, desc)
 
         aria_project_dict['working_directory'] = work_dir

version.py

 # Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev1
\ No newline at end of file
+__version__=v0.1.11-dev2
\ No newline at end of file