add singularity tests

Author: karlnyr

tests/utils/test_jobcreator.py

@@ -95,3 +95,28 @@ def test_project_job(subproc, testdata):
         )
         jc.project_job()
 
+def test_singularity_exec_binds_finishdir(testdata):
+    """finishdir is automatically added to the --bind list of every singularity exec call."""
+    jc = Job_Creator(
+        run_settings={'input': '/tmp/', 'finishdir': '/tmp/test_runfolder'},
+        config=preset_config,
+        log=logger,
+        sampleinfo=testdata,
+    )
+    cmd = jc._singularity_exec('blast', 'blastn -help')
+    assert '/tmp/test_runfolder' in cmd
+
+
+def test_singularity_exec_does_not_duplicate_finishdir(testdata):
+    """finishdir is not listed twice when it already appears in config bind_paths."""
+    config = dict(preset_config)
+    config['singularity'] = dict(preset_config['singularity'])
+    config['singularity']['bind_paths'] = ['/tmp/test_runfolder', '/data']
+    jc = Job_Creator(
+        run_settings={'input': '/tmp/', 'finishdir': '/tmp/test_runfolder'},
+        config=config,
+        log=logger,
+        sampleinfo=testdata,
+    )
+    cmd = jc._singularity_exec('blast', 'blastn -help')
+    assert cmd.count('/tmp/test_runfolder') == 1