Add test code for stats output file

tests/test_stats_output.py

+#!/usr/bin/env python
+
+import pathlib
+import pytest
+import os
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_exists(workflow_dir):
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    assert os.path.exists(full_path)
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_name(workflow_dir):
+    """ Read in the stats file and do some tests """
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    # Since we only have two lines in the test stats file, this works
+    with open(full_path, 'r') as fin:
+        header = next(fin).strip().split('\t')
+        values = next(fin).strip().split('\t')
+    data = dict(zip(header, values))
+
+    assert data['sample_name'] == 'micro'
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_mapped_reads(workflow_dir):
+    """ Read in the stats file and do some tests """
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    # Since we only have two lines in the test stats file, this works
+    with open(full_path, 'r') as fin:
+        header = next(fin).strip().split('\t')
+        values = next(fin).strip().split('\t')
+    data = dict(zip(header, values))
+
+    assert data['mapped_reads'] == '15515'
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_mapped_bases(workflow_dir):
+    """ Read in the stats file and do some tests """
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    # Since we only have two lines in the test stats file, this works
+    with open(full_path, 'r') as fin:
+        header = next(fin).strip().split('\t')
+        values = next(fin).strip().split('\t')
+    data = dict(zip(header, values))
+
+    assert data['mapped_bases'] == '2275114'
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_usable_reads(workflow_dir):
+    """ Read in the stats file and do some tests """
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    # Since we only have two lines in the test stats file, this works
+    with open(full_path, 'r') as fin:
+        header = next(fin).strip().split('\t')
+        values = next(fin).strip().split('\t')
+    data = dict(zip(header, values))
+
+    assert data['usable_reads'] == '15477'
+
+
+@pytest.mark.workflow(name='test-integration-no-cluster')
+def test_stats_file_usable_bases(workflow_dir):
+    """ Read in the stats file and do some tests """
+    stats_file = 'stats.tsv'
+    full_path = workflow_dir / pathlib.Path(stats_file)
+    # Since we only have two lines in the test stats file, this works
+    with open(full_path, 'r') as fin:
+        header = next(fin).strip().split('\t')
+        values = next(fin).strip().split('\t')
+    data = dict(zip(header, values))
+
+    assert data['usable_bases'] == '2270739'