Merge branch 'nG6_ont-qc_bug-and-visu' into 'master'

N g6 ont qc bug and visu

See merge request !21

workflows/ont_qc/__init__.py

@@ -30,7 +30,7 @@ class OntQualityCheck (NG6Workflow):
     def define_parameters(self, function="process"):
         logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
         self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz")
-        self.add_parameter("nb_threads", "Number of threads to use for porechop (default=16).", default=16)
+        self.add_parameter("trimming", "use trimming with porechop or not",choices= [ "yes", "no"], default = "no")
         self.add_parameter("fileformat", "The file format for porechop (default=fastq).", choices= [ "fastq", "fasta"], default = "fastq")
         self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
         self.add_parameter("barcoded", "Barcoded run or not", choices= [ "yes", "no"], default = "no")
@@ -52,7 +52,8 @@ class OntQualityCheck (NG6Workflow):
         addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.get_all_reads(), self.compression])
         #nanoplot = self.add_component("Nanoplot", [sample.name,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
         ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
-        trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.nb_threads, self.fileformat , "discard_middle"])
+        if self.trimming == "yes":
+            trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.fileformat , "discard_middle"])
         if self.fast5dir != None:
             fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive.tar"])
 

workflows/ont_qc/components/trimporechop.py

@@ -31,7 +31,6 @@ class Trim_porechop (Analysis):
 
     def define_parameters(self, fastq_files, nbthreads, formatfile, discard_middle, archivename="porechop_archive.tar"):
         self.add_input_file_list( "fastq_files", "fastq_files", default=fastq_files, required=True, file_format = 'fastq')
-        self.add_parameter("nbthreads", "number of threads to use (default=16)", default=16, type='int')
         self.add_parameter("formatfile", "format of the input files", default="fastq", type='str')
         self.add_parameter("discard_middle", "discard_middle", default="discard_middle", choices=[ "discard_middle", "do_not_discard_middle"])
         self.add_parameter("archive_name", "Name of the archive", default=archivename, type='str')
@@ -148,7 +147,7 @@ class Trim_porechop (Analysis):
 
             # Create cmd
             [cmd_inputs_pattern, next_arg_number] = get_argument_pattern(file_group, 0)
-            self.add_shell_execution(self.get_exec_path("porechop") +" " + self.options +  " --input ${" + str(next_arg_number) + "} --output ${" + str(next_arg_number+1) + "} --format " + self.formatfile + " --threads " + str(self.nbthreads) + " > " +" ${" + str(next_arg_number+2) + "}",
+            self.add_shell_execution(self.get_exec_path("porechop") +" " + self.options +  " -t 16 --input ${" + str(next_arg_number) + "} --output ${" + str(next_arg_number+1) + "} --format " + self.formatfile + " --threads " + str(self.nbthreads) + " > " +" ${" + str(next_arg_number+2) + "}",
                                 cmd_format='{EXE} {IN} {OUT}' ,
                                 map=False,
                                 inputs = file_group,