Add new '-z' option and fix bug with rerun.

workflows/components/flash.py

@@ -152,16 +152,6 @@ class Flash (Analysis):
         return stdout.split()[1]
 
     def process(self):
-        # Creates list for temporary uncompressed files
-        tmp_extended_frags = self.get_outputs('{basename_woext}.extendedFrags.fastq', self.prefixes)
-        tmp_not_combined_read_1 = self.get_outputs('{basename_woext}.notCombined_1.fastq', self.prefixes)
-        tmp_not_combined_read_2 = self.get_outputs('{basename_woext}.notCombined_2.fastq', self.prefixes)
-  
-        # Join pairs
         for i in range(0, len(self.prefixes)):
-            flash = ShellFunction(self.get_exec_path("flash") + " $1 $2 " + self.options + " -o " + os.path.basename(self.prefixes[i]) + " -d " + self.output_directory + " 2> $3", cmd_format='{EXE} {IN} {OUT}')
-            flash(inputs = [self.read1_files[i], self.read2_files[i]], outputs = [self.stderrs[i], tmp_extended_frags[i], tmp_not_combined_read_1[i], tmp_not_combined_read_2[i]])
-        
-        # Compress files
-        compress = ShellFunction("gzip $1 $2 $3", cmd_format='{EXE} {IN} {OUT}')
-        compress = MultiMap(compress, inputs = [tmp_extended_frags, tmp_not_combined_read_1, tmp_not_combined_read_2], outputs = [self.extended_frags, self.not_combined_read_1, self.not_combined_read_2])
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+            flash = ShellFunction(self.get_exec_path("flash") + " -z $1 $2 " + self.options + " -o " + os.path.basename(self.prefixes[i]) + " -d " + self.output_directory + " 2> $3", cmd_format='{EXE} {IN} {OUT}')
+            flash( inputs=[self.read1_files[i], self.read2_files[i]], outputs=[self.stderrs[i], self.extended_frags[i], self.not_combined_read_1[i], self.not_combined_read_2[i]] )
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