WIP: Adding support for NextSeq

README.md

@@ -22,10 +22,12 @@ Instrument types supported in checkQC are the following:
  - HiSeq2500
  - MiSeq
  - NovaSeq
+ - ISeq
+ - NextSeq
 
 Install instructions
 --------------------
-CheckQC **requires Python 3.5** (or higher to run). CheckQC can be installed with pip.
+CheckQC **requires Python 3.5 or Python3.6**. CheckQC can be installed with pip.
 
 ```
 pip install checkqc

checkQC/default_config/config.yaml

@@ -316,7 +316,7 @@ miseq_v3:
         error: 9 # 50 % of threshold for clusters pass filter
 
 iseq_v1:
-  300:
+  301:
     handlers:
       - name: ClusterPFHandler
         warning: 4 # Millons of clusters
@@ -331,3 +331,38 @@ iseq_v1:
       - name: ReadsPerSampleHandler
         warning: unknown
         error: 2 # 50 % of threshold for clusters pass filter
+
+# TODO The nextseq really has a high and a mid-output mode.
+#      This needs to be supported here later.
+#      /JD 2018-09-13
+nextseq_v1:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 400 # Millons of clusters
+        error: unknown
+      - name: Q30Handler
+        warning: 80 # Give percentage for reads greater than Q30
+        error: unknown # Give percentage for reads greater than Q30
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 200 # 50 % of threshold for clusters pass filter
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 400 # Millons of clusters
+        error: unknown
+      - name: Q30Handler
+        warning: 75 # Give percentage for reads greater than Q30
+        error: unknown # Give percentage for reads greater than Q30
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 200 # 50 % of threshold for clusters pass filter

checkQC/run_type_recognizer.py

@@ -56,6 +56,15 @@ def reagent_version(runtype_recognizer):
         """
         raise NotImplementedError
 
+class NextSeq(IlluminaInstrument):
+    @staticmethod
+    def name():
+        return "nextseq"
+
+    @staticmethod
+    def reagent_version(runtype_recognizer):
+        return "v1"
+
 class ISeq(IlluminaInstrument):
 
     @staticmethod
@@ -176,7 +185,8 @@ def instrument_type(self):
                                  "D": "hiseq2500",
                                  "ST": "hiseqx",
                                  "A": "novaseq",
-                                 "FFSP": "iseq"}
+                                 "FFSP": "iseq",
+                                 "NS": "nextseq"}
 
         for key, value in machine_type_mappings.items():
             if instrument_name.startswith(key):

tests/test_run_type_recognizer.py

@@ -4,7 +4,7 @@
 import os
 
 from checkQC.exceptions import RunModeUnknown, ReagentVersionUnknown
-from checkQC.run_type_recognizer import RunTypeRecognizer, HiSeq2500, MiSeq, NovaSeq, ISeq
+from checkQC.run_type_recognizer import RunTypeRecognizer, HiSeq2500, MiSeq, NovaSeq, ISeq, NextSeq
 from checkQC.runfolder_reader import RunfolderReader
 
 
@@ -48,6 +48,11 @@ def test_returns_iseq(self):
         actual = runtyperecognizer.instrument_type()
         self.assertTrue(isinstance(actual, ISeq))
 
+    def test_returns_nextseq(self):
+        runtyperecognizer = self._create_runtype_recognizer("NS500559")
+        actual = runtyperecognizer.instrument_type()
+        self.assertTrue(isinstance(actual, NextSeq))
+
 
 class TestIlluminaInstrument(TestCase):
 
@@ -60,6 +65,7 @@ def setUp(self):
         self.miseq = MiSeq()
         self.novaseq = NovaSeq()
         self.iseq = ISeq()
+        self.nextseq = NextSeq()
 
     def test_all_is_well(self):
         runtype_dict = {"RunParameters": {"Setup": {"RunMode": "RapidHighOutput", "Sbs": "HiSeq SBS Kit v4"}}}
@@ -117,3 +123,7 @@ def test_novaseq_reagent_version_raises(self):
 
         with self.assertRaises(ReagentVersionUnknown):
             self.novaseq.reagent_version(mock_runtype_recognizer)
+
+    def test_nextseq(self):
+        self.assertEqual(self.nextseq.name(), "nextseq")
+        self.assertEqual(self.nextseq.reagent_version(self.MockRunTypeRecognizer(None)), "v1")