fixed issues with refgenie test

nf_core/refgenie.py

@@ -7,7 +7,8 @@
 import os
 import re
 import rich
-import refgenconf
+
+# import refgenconf
 from warnings import warn
 from rich.logging import RichHandler
 import nf_core.utils
@@ -47,7 +48,8 @@ def _print_nf_config(rgc):
         for asset in asset_list:
             try:
                 pth = rgc.seek(genome, asset)
-            except refgenconf.exceptions.MissingSeekKeyError:
+            # Catch general exception instead of refgencof exception --> no refgenconf import needed
+            except Exception as e:
                 log.warn(f"{genome}/{asset} is incomplete, ignoring...")
             else:
                 genomes_str += '      {} = "{}"\n'.format(asset.ljust(20, " "), pth)

tests/test_refgenie.py

@@ -2,17 +2,13 @@
 """ Tests covering the refgenie integration code
 """
 
-import nf_core.refgenie
-import refgenconf
-import json
 import os
-import pytest
-import time
 import unittest
 import tempfile
-from unittest import mock
 import subprocess
-from rich.console import Console
+import shlex
+
+import nf_core.refgenie
 
 
 class TestRefgenie(unittest.TestCase):
@@ -33,18 +29,18 @@ def setUp(self):
         # Initialize a refgenie config
         os.system(f"refgenie init -c {self.REFGENIE}")
 
-        # Populate the config with a genome
-        os.system(f"refgenie pull t7/fasta -c {self.REFGENIE}")
-
+        # Add NXF_REFGENIE_PATH to refgenie config
         with open(self.REFGENIE, "a") as fh:
-            fh.write(f"nextflow_config: {os.path.join(self.NXF_REFGENIE_PATH)}")
+            fh.write(f"nextflow_config: {os.path.join(self.NXF_REFGENIE_PATH)}\n")
 
     def tearDown(self) -> None:
         # Remove the tempdir again
         os.system(f"rm -rf {self.tmp_dir}")
 
     def test_update_refgenie_genomes_config(self):
         """Test that listing pipelines works"""
-        rgc = refgenconf.RefGenConf(self.REFGENIE)
+        # Populate the config with a genome
+        cmd = f"refgenie pull t7/fasta -c {self.REFGENIE}"
+        out = subprocess.check_output(shlex.split(cmd), stderr=subprocess.STDOUT)
 
-        assert nf_core.refgenie.update_config(rgc) == True
+        assert "Updated nf-core genomes config" in str(out)