Apply suggestions from code review

Co-authored-by: Cunliang Geng <c.geng@esciencecenter.nl>

src/nplinker/data/nplinker.toml

@@ -56,7 +56,8 @@ version = 1
 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
 # for version 2, use the following parameters string:
 # parameters = "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30"
-# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the "cluster" subcommand to be used.
+# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the "cluster" subcommand and its parameters to be used. 
+NPLinker will automatically set the following parameters: `--pfam_path`, `--inputdir` and `--outputdir`. So, do not set them here.
 # BiG-SCPAPE v2 also runs a --mix analysis by default, and does not need this to be included.
 # Which bigscape cutoff to use for NPLinker analysis.
 # There might be multiple cutoffs in bigscape output.

tests/unit/genomics/test_runbigscape.py

@@ -17,9 +17,9 @@ def test_run_bigscape(tmp_path, version):
     assert result is True
 
 
+@pytest.mark.skipif(os.getenv('GITHUB_ACTIONS') == 'true', reason="The test is time-consuming on CI")
 @pytest.mark.parametrize("version", [1, 2])
 def test_run_bigscape_small_dataset(tmp_path, version):
-    pytest.skip("This test is too slow to run in CI")
     result = bigscape.run_bigscape(
         antismash_path=DATA_DIR / "bigscape" / "minimal_dataset",
         output_path=tmp_path,