probleme lorsqu'input ustack vide ou avec peu de données, le clustering ne...

probleme lorsqu'input ustack vide ou avec peu de données, le clustering ne fonctionne pas et ustacks ne crée pas de fichiers de sorties.

workflows/radseq/components/ustacks.py

@@ -48,7 +48,8 @@ class Ustacks (Analysis):
         self.alleles = OutputFileList(self.get_outputs('{basename_woext}.alleles.tsv', self.read1_files))
         self.snps = OutputFileList(self.get_outputs('{basename_woext}.snps.tsv', self.read1_files))
         self.stderrs = OutputFileList(self.get_outputs('{basename_woext}.stderrs', self.read1_files))
-    
+        print self.tags, self.alleles, self.snps
+        
     def define_analysis(self):
         self.name = "ustacks"
         self.description = "Locus prediction per individus"
@@ -75,12 +76,15 @@ class Ustacks (Analysis):
     def process(self):
         for idx, input in enumerate(self.read1_files):
             parts = os.path.splitext(os.path.basename(input))
-            indiv = parts [0]
+            indiv = parts[0]
             if parts[1] == ".gz" :
                 indiv = os.path.splitext(parts[0])
             indiv = re.sub( r'_1$', '', indiv)
             individ = self.indiv_dic[indiv]["id"]
             format = "fastq" if os.path.splitext(os.path.basename(input))[1] != ".gz" else "gzfastq"
+            #tmp_function=ShellFunction("echo $1 >$2", cmd_format='{IN} {OUT}')
+            #tmp_function(inputs = input, outputs = [self.tags[idx]])
+            
             ustacks = ShellFunction(self.get_exec_path("ustacks") + " -t " + format + " -f $1 -d -r -o " + self.output_directory + " -i " + str(individ) + 
                                     " -m " + str(self.min_cov) + " -M " + str(self.primary_mismatch) + " -N " + str(self.secondary_mismatch) + 
                                     " 2> $2", cmd_format='{EXE} {IN} {OUT}')