Update tests and add missing files

src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy

@@ -139,6 +139,32 @@ class NanoporeParserSpec extends Specification {
     assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL"
   }
 
+  def "parsing a valid minimal file structure with bam files and dorado basecalling returns an OxfordNanoporeExperiment"() {
+    given:
+    def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_minimal_bam")
+    when:
+    def experiment = NanoporeParser.parseFileStructure(pathToDirectory)
+    then:
+    assert experiment instanceof OxfordNanoporeExperiment
+    // Check that the metadata from the report file has been retrieved
+    assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094"
+    // Check that the metadata from the summary file has been retrieved
+    assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL"
+  }
+
+  def "parsing a valid minimal file structure with pod5 files and dorado basecalling returns an OxfordNanoporeExperiment"() {
+    given:
+    def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_minimal_pod5")
+    when:
+    def experiment = NanoporeParser.parseFileStructure(pathToDirectory)
+    then:
+    assert experiment instanceof OxfordNanoporeExperiment
+    // Check that the metadata from the report file has been retrieved
+    assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094"
+    // Check that the metadata from the summary file has been retrieved
+    assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL"
+  }
+
   def "parsing a valid file structure for dorado based basecalling containing additional unknown files and folder still returns an OxfordNanoporeExperiment Object"() {
     given:
     def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example")

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5

@@ -0,0 +1 @@
+This is some text