diff --git a/microview/file_finder.py b/microview/file_finder.py index 5edd42f..8c2ec55 100644 --- a/microview/file_finder.py +++ b/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 diff --git a/tests/conftest.py b/tests/conftest.py index 3041467..2fc5e42 100644 --- a/tests/conftest.py +++ b/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 diff --git a/tests/test_data/centrifuge_test.tsv b/tests/test_data/centrifuge_test.txt similarity index 100% rename from tests/test_data/centrifuge_test.tsv rename to tests/test_data/centrifuge_test.txt diff --git a/tests/test_data/contrast_table.csv b/tests/test_data/contrast_table.csv index 3d96436..a893a0a 100644 --- a/tests/test_data/contrast_table.csv +++ b/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 diff --git a/tests/test_data/kaiju_test.tsv b/tests/test_data/kaiju_test.txt similarity index 100% rename from tests/test_data/kaiju_test.tsv rename to tests/test_data/kaiju_test.txt diff --git a/tests/test_data/kaiju_test_2.tsv b/tests/test_data/kaiju_test_2.txt similarity index 100% rename from tests/test_data/kaiju_test_2.tsv rename to tests/test_data/kaiju_test_2.txt diff --git a/tests/test_data/kraken_test.tsv b/tests/test_data/kraken_test.txt similarity index 100% rename from tests/test_data/kraken_test.tsv rename to tests/test_data/kraken_test.txt