Ci

Add and improve CI

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors
• Docker images moved to production release and changed in pipeline
• Docker images used in the CI unit tests match those used in pipleine

• Close issue
  Closes #27 (closed) Closes #48 (closed) Closes #54 (closed)

/cc @ghenry @venkat.malladi

workflow/tests/test_consistency.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../../'
+
+@pytest.mark.consistencySE
+def test_consistencySE():
+    assert os.path.exists(os.path.join(test_output_path, 'SE_multiqc_data.json'))
+    assert readAssigned("assignedSE.txt","assignedExpectSE.txt")
+
+@pytest.mark.consistencyPE
+def test_consistencyPE():
+    assert os.path.exists(os.path.join(test_output_path, 'PE_multiqc_data.json'))
+    assert readAssigned("assignedPE.txt","assignedExpectPE.txt")
+
+def readAssigned(fileAssigned,fileExpectAssigned):
+    data = False
+    assigned = open(fileAssigned, "r")
+    expect = open(fileExpectAssigned, "r")
+    lineAssigned = assigned.readline()
+    lineExpect = expect.readline()
+    if lineAssigned.strip() == lineExpect.strip():
+        data = True
+
+    return data