From db6e02a63506df861d6765bbc1c31085b64ee11e Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
Date: Wed, 31 Jan 2024 21:11:59 +0100
Subject: [PATCH] fix

---
 tests/files/zarp/workflow/Snakefile          | 21 ++++++++++++++++++++
 tests/files/zarp/workflow/rules/htsinfer.smk |  9 ++++-----
 tests/test_cli.py                            |  2 +-
 3 files changed, 26 insertions(+), 6 deletions(-)
 create mode 100644 tests/files/zarp/workflow/Snakefile

diff --git a/tests/files/zarp/workflow/Snakefile b/tests/files/zarp/workflow/Snakefile
new file mode 100644
index 0000000..97d2fc7
--- /dev/null
+++ b/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}'
+
diff --git a/tests/files/zarp/workflow/rules/htsinfer.smk b/tests/files/zarp/workflow/rules/htsinfer.smk
index f2a4385..108a06c 100644
--- a/tests/files/zarp/workflow/rules/htsinfer.smk
+++ b/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}'
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 778c142..9aed37d 100644
--- a/tests/test_cli.py
+++ b/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."""