diff --git a/tests/test_scripts_dgicev.py b/tests/test_scripts_dgicev.py index 76381a5..4326bb1 100644 --- a/tests/test_scripts_dgicev.py +++ b/tests/test_scripts_dgicev.py @@ -9,7 +9,7 @@ import pytest -@pytest.mark.optional +@pytest.mark.skip(reason="Only for testing purposes") def bam_to_sam(bam_file): """Converts a BAM file to SAM format and returns it as a string. @@ -28,7 +28,7 @@ def bam_to_sam(bam_file): return temp_sam.read().decode() -@pytest.mark.optional +@pytest.mark.skip(reason="Only for testing purposes") def test_read_run_error_free(): """Test the read.py script by piping SAM data to it.""" input_bam = "tests/data/REF_aln_trim_subsample.bam" diff --git a/tests/test_silo_input_transformer.py b/tests/test_silo_input_transformer.py index 521ba2b..45df493 100644 --- a/tests/test_silo_input_transformer.py +++ b/tests/test_silo_input_transformer.py @@ -6,8 +6,6 @@ import pytest -import silo_input_transformer - logging.basicConfig(level=logging.INFO) config_path = "silo_input_transformer/config.yaml" @@ -18,6 +16,9 @@ ) def test_transform(): """Test to run Rust based Silo input transformer, fail for error.""" + + import silo_input_transformer + result = silo_input_transformer.run_with_config(config_path) # type: ignore logging.info(f"Result from Rust: {result}") return result