whitespace-cleanup

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index d1a40bdb408897a271ffaeb87f753f2aab468f61..9fef5d1bb473d5e6f689ba76ea839d39311482b4 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -189,10 +189,10 @@ class CASAVA(Alignment):
             return None
         time_element = self.tree.xpath('TIME_STAMP')
         if len(time_element) == 1:
-           timetuple = time.strptime(
-               time_element[0].text.strip(),
-               "%a %b %d %H:%M:%S %Y")
-           return datetime(*timetuple[:6])
+            timetuple = time.strptime(
+                time_element[0].text.strip(),
+                "%a %b %d %H:%M:%S %Y")
+            return datetime(*timetuple[:6])
         return super(CASAVA, self)._get_date()
     date = property(_get_date)
 

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index 03e71f9bf64c65d0a34ef9fe6db3141e797afe93..52dda0889c9b8cfc5aea23c6423e32beb2f9e1fa 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -89,7 +89,7 @@ class IPAR(object):
         else:
             return runfolder[0].text
     runfolder_name = property(_get_runfolder_name)
-    
+
     def _get_software(self):
         """Return software name"""
         if self.tree is None:
@@ -197,7 +197,7 @@ class IPAR(object):
             if element.tag == IPAR.RUN:
                 self.tree = element
             elif element.tag == IPAR.TIMESTAMP:
-               self.time = int(element.text)
+                self.time = int(element.text)
             elif element.tag == IPAR.MATRIX:
                 self.matrix = element.text
             else:

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index dfc75f4b0f44492338458df766a6f6c4039fe301..7acb294dcb2484cacef3bfa7ca09133dbda7cbcc 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -30,7 +30,7 @@ from htsworkflow.pipelines import srf
 
 class PipelineRun(object):
     """Capture "interesting" information about a pipeline run
-    
+
     :Variables:
       - `pathname` location of the root of this runfolder
       - `serialization_filename` read only property containing name of run xml file
@@ -46,12 +46,12 @@ class PipelineRun(object):
 
     def __init__(self, pathname=None, flowcell_id=None, xml=None):
         """Initialize a PipelineRun object
-        
+
         :Parameters:
           - `pathname` the root directory of this run folder.
           - `flowcell_id` the flowcell ID in case it can't be determined
           - `xml` Allows initializing an object from a serialized xml file.
-          
+
         :Types:
           - `pathname` str
           - `flowcell_id` str
@@ -74,7 +74,7 @@ class PipelineRun(object):
 
     def _get_flowcell_id(self):
         """Return the flowcell ID
-        
+
         Attempts to find the flowcell ID through several mechanisms.
         """
         # extract flowcell ID
@@ -96,7 +96,7 @@ class PipelineRun(object):
 
     def _get_flowcell_id_from_flowcellid(self):
         """Extract flowcell id from a Config/FlowcellId.xml file
-        
+
         :return: flowcell_id or None if not found
         """
         config_dir = os.path.join(self.pathname, 'Config')
@@ -139,9 +139,9 @@ class PipelineRun(object):
 
     def _get_run_dirname(self):
         """Return name of directory to hold result files from one analysis
-        
+
         For pre-multiplexing runs this is just the cycle range C1-123
-        For post-multiplexing runs the "suffix" that we add to 
+        For post-multiplexing runs the "suffix" that we add to
         differentiate runs will be added to the range.
         E.g. Unaligned_6mm may produce C1-200_6mm
         """
@@ -158,7 +158,7 @@ class PipelineRun(object):
 
     def get_elements(self):
         """make one master xml file from all of our sub-components.
-        
+
         :return: an ElementTree containing all available pipeline
                  run xml compoents.
         """
@@ -202,10 +202,10 @@ class PipelineRun(object):
 
     def _get_serialization_filename(self):
         """Compute the filename for the run xml file
-        
-        Attempts to find the latest date from all of the run 
+
+        Attempts to find the latest date from all of the run
         components.
-        
+
         :return: filename run_{flowcell id}_{timestamp}.xml
         :rtype: str
         """
@@ -219,7 +219,7 @@ class PipelineRun(object):
 
     def save(self, destdir=None):
         """Save a run xml file.
-        
+
         :param destdir: Directory name to save too, uses current directory
                         if not specified.
         :type destdir: str
@@ -234,10 +234,10 @@ class PipelineRun(object):
 
     def load(self, filename):
         """Load a run xml into this object.
-        
+
         :Parameters:
           - `filename` location of a run xml file
-          
+
         :Types:
           - `filename` str
         """
@@ -260,7 +260,7 @@ def load_pipeline_run_xml(pathname):
 
 def get_runs(runfolder, flowcell_id=None):
     """Find all runs associated with a runfolder.
-    
+
     We end up with multiple analysis runs as we sometimes
     need to try with different parameters. This attempts
     to return a list of all the various runs.
@@ -367,7 +367,7 @@ def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
                 p.gerald = gerald.gerald(aligned)
             runs.append(p)
         except (IOError, RuntimeError) as e:
-           LOGGER.error("Exception %s", str(e))
+            LOGGER.error("Exception %s", str(e))
             LOGGER.error("Skipping run in %s", flowcell_id)
     return len(runs) - start
 
@@ -543,8 +543,8 @@ def summary_report(runs):
     for run in runs:
         # print a run name?
         report.append('Summary for %s' % (run.serialization_filename,))
-       # sort the report
-       if run.gerald:
+        # sort the report
+        if run.gerald:
             eland_keys = sorted(run.gerald.eland_results.keys())
         else:
             report.append("Alignment not done, no report possible")
@@ -831,6 +831,3 @@ def clean_runs(runs, dry_run=True):
             clean_process = subprocess.Popen(['make', 'clean_intermediate'],
                                              cwd=run.image_analysis.pathname,)
             clean_process.wait()
-
-
-