refactor: Detect txt instead of tsv files

- Will make it easier to integrate with existing nf-core modules

microview/file_finder.py

@@ -155,7 +155,7 @@ def find_reports(reports_path: Path, console) -> List[Sample]:
         List[Sample]: List of samples, an object comprising two attributes,
           one the report path, the other a string specifying the report type.
     """
-    file_paths: List[Path] = list(reports_path.glob("*tsv"))
+    file_paths: List[Path] = list(reports_path.glob("*txt"))
     samples = detect_report_type(file_paths, console)
     return samples
 

tests/conftest.py

@@ -38,17 +38,17 @@ def all_sample_counts():
 
 @pytest.fixture
 def get_kraken_data():
-    return Path(__file__).parent.resolve() / "test_data" / "kraken_test.tsv"
+    return Path(__file__).parent.resolve() / "test_data" / "kraken_test.txt"
 
 
 @pytest.fixture
 def get_kaiju_data():
-    return Path(__file__).parent.resolve() / "test_data" / "kaiju_test.tsv"
+    return Path(__file__).parent.resolve() / "test_data" / "kaiju_test.txt"
 
 
 @pytest.fixture
 def get_centrifuge_data():
-    return Path(__file__).parent.resolve() / "test_data" / "centrifuge_test.tsv"
+    return Path(__file__).parent.resolve() / "test_data" / "centrifuge_test.txt"
 
 
 @pytest.fixture

tests/test_data/contrast_table.csv

@@ -1,3 +1,3 @@
 sample,group
-kaiju_test.tsv,one
-kaiju_test_2.tsv,two
+kaiju_test.txt,one
+kaiju_test_2.txt,two