Update Samtools version :

Change samtools sort option
adding of -o, and removing of the renaming of the output

workflows/components/bwa.py

@@ -92,14 +92,14 @@ class BWA (Analysis):
             if self.read2:
                 self.add_shell_execution(self.get_exec_path("bwa") + " " + self.algorithm + " " + self.reference_genome + 
                                 " $1 $2 2>> $4 | " + self.get_exec_path("samtools") + " view -bS - | " + 
-                                self.get_exec_path("samtools") + " sort - $3 2>> $4; mv $3.bam $3;", 
+                                self.get_exec_path("samtools") + " sort - -o $3 2>> $4;", 
                                 cmd_format='{EXE} {IN} {OUT}' , map=True,
                                 inputs=[self.read1, self.read2], outputs=[unmerged_bam, self.stderrs], includes=self.reference_genome)
             # Single-end
             else:
                 self.add_shell_execution(self.get_exec_path("bwa") + " " + self.algorithm + " " + self.reference_genome + 
                                     " $1 2>> $3 | " + self.get_exec_path("samtools") + " view -bS - | " + 
-                                    self.get_exec_path("samtools") + " sort - $2 2>> $3 ; mv $2.bam $2;", 
+                                    self.get_exec_path("samtools") + " sort - -o $2 2>> $3 ;", 
                                 cmd_format='{EXE} {IN} {OUT}' , map=True,
                                 inputs=[self.read1], outputs=[unmerged_bam, self.stderrs], includes=self.reference_genome)
 
@@ -118,7 +118,7 @@ class BWA (Analysis):
                                          inputs=[reads], outputs=[sais, self.stderrs_aln], includes=self.reference_genome)
                 self.add_shell_execution(self.get_exec_path("bwa") + " sampe " + self.reference_genome + 
                                          " $1 $2 $3 $4 2>> $6 | " + self.get_exec_path("samtools") + " view -bS - | " + 
-                                         self.get_exec_path("samtools") + " sort - $5 2>> $6; mv $5.bam $5;",
+                                         self.get_exec_path("samtools") + " sort - -o $5 2>> $6;",
                                          cmd_format='{EXE} {IN} {OUT}', map=True,
                                          inputs=[self.sai1, self.sai2, self.read1, self.read2], outputs=[unmerged_bam, self.stderrs], includes=self.reference_genome)
             # Single-end
@@ -128,7 +128,7 @@ class BWA (Analysis):
                                          inputs=[reads], outputs=[sais, self.stderrs_aln], includes=self.reference_genome)
                 self.add_shell_execution(self.get_exec_path("bwa") + " samse " + self.reference_genome + 
                                          " $1 $2 2>> $4 | " + self.get_exec_path("samtools") + " view -bS - | " + 
-                                         self.get_exec_path("samtools") + " sort - $3 2>> $4; mv $3.bam $3;", 
+                                         self.get_exec_path("samtools") + " sort - -o $3 2>> $4;", 
                                          cmd_format='{EXE} {IN} {OUT}', map=True,  
                                          inputs=[self.sai1, self.read1], outputs=[unmerged_bam, self.stderrs], includes=self.reference_genome)
 

workflows/illumina_rnaseq/components/star.py

@@ -76,7 +76,7 @@ class STAR (Analysis):
         
         # sort
         self.add_shell_execution( self.get_exec_path("samtools") + ' view -Sb $1 | ' + self.get_exec_path("samtools") + 
-                                 ' sort -@ ' + str(self.n_threads) + ' -f - $2 ' ,  cmd_format='{EXE} {IN} {OUT}', map=True,
+                                 ' sort -@ ' + str(self.n_threads) + ' -f - -o $2 ' ,  cmd_format='{EXE} {IN} {OUT}', map=True,
                                  inputs = [self.output_sams_no_md], outputs = [self.output_sorted_bams])
         
         #calmd and convert to bam

[Maxime Manno]

link to the issue #7 (closed)