From 3065da66eb3d3d9daa1ac776e8ea1843b75da428 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 23 Apr 2019 07:46:30 -0500
Subject: [PATCH] Fix test file error and missing modules.
---
workflow/main.nf | 2 ++
workflow/tests/test_generate_software_references.py | 11 ++++++++++-
2 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index ca8736f..99474e5 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -326,6 +326,8 @@ process crossReads {
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load phantompeakqualtools/1.2
python3 $baseDir/scripts/xcor.py -t $seTagAlign
"""
}
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index 6891bf9..ce3640c 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/workflow/tests/test_generate_software_references.py
@@ -11,4 +11,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_software_references():
- assert os.path.exists(os.path.join(test_output_path, 'software_references_mqc.txt'))
+ assert os.path.exists(os.path.join(test_output_path, 'software_references_mqc.yaml'))
+
+
+@pytest.mark.singleend
+def test_software_references_output():
+ software_references = os.path.join(test_output_path, 'software_references_mqc.yaml')
+ with open(software_references, 'r') as stream:
+ data_loaded = yaml.load(stream)
+
+ assert len(data_loaded['data'].split('<dt>')) == 17
--
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