fix

tests/files/zarp/workflow/Snakefile

@@ -0,0 +1,21 @@
+"""Dummy version of Snakefile for ZARP workflow."""
+
+
+localrules:
+    dummy,
+    all,
+
+
+rule all:
+    input:
+        "zarp_dummy_output",
+
+
+rule dummy:
+    input:
+        config["samples"],
+    output:
+        "zarp_dummy_output",
+    shell:
+        'cat {input} > {output}'
+

tests/files/zarp/workflow/rules/htsinfer.smk

@@ -1,7 +1,4 @@
-"""
-Dummy version of Snakefile for downloading inferring RNA-Seq sample
-metadata with HTSinfer.
-"""
+"""Dummy version of Snakefile for inferring sample metadata with HTSinfer."""
 
 
 localrules:
@@ -15,8 +12,10 @@ rule all:
 
 
 rule dummy:
+    input:
+        config["samples"],
     output:
         config["samples_out"],
     shell:
-        'echo "sample\tfq1" > {output}'
+        'cat {input} > {output}'
 

tests/test_cli.py

@@ -59,7 +59,7 @@ def test_normal_mode_with_args(self, monkeypatch, tmpdir):
         )
         with pytest.raises(SystemExit) as exc:
             main()
-        assert exc.value.code == 1
+        assert exc.value.code == 0
 
     def test_normal_mode_with_runtime_error(self, monkeypatch, tmpdir):
         """Call with runtime error being raised."""