Add Illumina_10X workflow

workflows/illumina_10X/__init__.py

+#
+# Copyright (C) 2012 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+import os
+import sys
+import re
+import logging
+from ng6.ng6workflow import CasavaNG6Workflow
+from ng6.utils import Utils
+
+
+class Illumina10XQualityCheck (CasavaNG6Workflow):
+
+    def get_name(self):
+        return 'illumina_10X_qc'
+
+    def get_description(self):
+        return "illumina quality check pipeline for 10X analyses"
+
+
+    def define_parameters(self, function="process"):
+        self.add_input_file("reference_genome", "Which genome should the read being align on")
+
+
+    def process(self):
+        fastqilluminafilter, filtered_read1_files, filtered_read2_files, concat_files = self.illumina_process()
\ No newline at end of file