Merge branch 'NGLLink' into 'master'

purge ONT fastq.gz during purge process

See merge request !157

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

@@ -212,7 +212,7 @@ class tx_nG6_utils {
                 return 0;
             }
     		#Exclusion of the log files from the purge process
-//     		$stream = ssh2_exec($connection, '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 {} \;');
+//     		$stream = ssh2_exec($connection, 'find '.$directory.' -maxdepth 1 -not -name "*.html" -not -name "*.png" -not -name "*.log" -not -name "*.log.gz" -not -name "*.pdf" -not -name "md5sum.txt" -name "*GXB02039*fastq.gz" -name "*PCT0078*fastq.gz" -type f -exec rm -f {} \;');
 //     		$errorStream = ssh2_fetch_stream($stream, SSH2_STREAM_STDERR);
 //     		// Enable blocking for both streams
 //     		stream_set_blocking($errorStream, true);

workflows/methylseq/components/bismark.py

@@ -99,8 +99,8 @@ class Bismark (Analysis):
                 # 2 bowtie process are launch in directional mode so divided allocated cpu for each bowtie
                 self.args += " --p "+ str(int(self.nb_proc/2))
             self.args += " --bowtie2"
-            if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
-                self.args += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
+            #if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
+            #    self.args += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
              
         
         self.options = self.args + " | Databank " + os.path.basename(self.reference_genome)

workflows/methylseq/components/bismark_genome_preparation.py

@@ -57,8 +57,8 @@ class BismarkGenomePreparation (Component):
         
         if not self.bowtie1 : 
             btw_param = " --bowtie2"
-            if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
-                btw_param += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
+            #if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
+            #    btw_param += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
             self.args += "\\'"+btw_param+"\\'"
             
         

workflows/methylseq/components/trim_galore.py

@@ -80,12 +80,12 @@ class TrimGalore (Analysis):
     def process(self):
         
         if self.is_paired: 
-            self.add_shell_execution( self.get_exec_path("trim_galore") + " " + self.options + \
+            self.add_shell_execution( "module load bioinfo/Cutadapt/1.8.3;module load bioinfo/TrimGalore/0.4.5;"+ self.get_exec_path("trim_galore") + " " + self.options + \
                             " -o " + self.output_directory + " $1 $2 >$3 2>> $4 ", 
                             cmd_format='{EXE} {IN} {OUT}', map=True, inputs=[self.input_files_R1, self.input_files_R2], 
                             outputs=[self.stderrs,self.stdouts,self.output_files_R1,self.output_files_R2,self.report_files_R1,self.report_files_R2])
         else : 
-            self.add_shell_execution( self.get_exec_path("trim_galore") + " " + self.options + \
+            self.add_shell_execution( "module load bioinfo/Cutadapt/1.8.3;module load bioinfo/TrimGalore/0.4.5;"+ self.get_exec_path("trim_galore") + " " + self.options + \
                             " -o " + self.output_directory + " $1 > $2 2>> $3 ", cmd_format='{EXE} {IN} {OUT}', map=True,
                             inputs=[self.input_files_R1], outputs=[self.stderrs,self.stdouts,self.output_files_R1,self.report_files_R1])