Merge branch 'NGLLink' into 'master'

do not save bismark bam files and files generated by and update purge policy

See merge request !158

.pydevproject

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?eclipse-pydev version="1.0"?><pydev_project>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+    
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+    
+    <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
+    
 </pydev_project>

ui/nG6/Classes/Controller/class.tx_nG6_utils.php

@@ -204,7 +204,7 @@ class tx_nG6_utils {
 //     			fclose($stream);
 //     			return 0;
 //     		}
-            $outputStream = $ssh->exec('find '.$directory.' -maxdepth 1 -not -name "*.html" -not -name "*.png" -not -name "*.log" -not -name "*.log.gz" -not -name "*.pdf" -not -name "md5sum.txt" -not -name "*GXB02039*" -not -name "*PCT0078*" -type f -exec rm -f {} \;');
+            $outputStream = $ssh->exec('find '.$directory.' -maxdepth 1 -not -name "*.html" -not -name "*.png" -not -name "*.log" -not -name "*.log.gz" -not -name "*.pdf" -not -name "md5sum.txt" -not -name "*GXB02039*" -not -name "*.sequencing_summary.txt*" -type f -exec rm -f {} \;');
             $errorStream = $ssh->getStdError();
             if($errorStream != "") {
                 return 1;

workflows/methylseq/components/bismark.py

@@ -132,7 +132,7 @@ class Bismark (Analysis):
                                 inputs=self.input_files_R1, outputs=[self.output_files,self.stderrs,self.output_report,self.output_bam], includes=self.reference_genome)
 
     def post_process(self):
-        self._save_files(self.output_bam)
+        #self._save_files(self.output_bam)
         results_files = self.output_report
         logging.getLogger("ng6").debug("bismark.post_process self.output_report = " + ",".join(self.output_report)) 
         # Finally create and add the archive to the analysis

workflows/methylseq/components/bismark_methylation_extractor.py

@@ -89,7 +89,7 @@ class BismarkMethylationExtractor (Analysis):
                if not file.endswith(".bam") :
                    methylationExtractorResultFiles.append(os.path.join(directory, file))
            #Not necesary
-           self._archive_files(methylationExtractorResultFiles,self.compression,os.path.basename(directory)+".tar") 
+           #self._archive_files(methylationExtractorResultFiles,self.compression,os.path.basename(directory)+".tar") 
            
     def __parse_report_file (self, report_file):
         logging.getLogger("ng6").debug("BismarkMethylationExtractor.__parse_report_file "  +report_file)