Add in test for utils.

workflow/tests/test_utils.py

+#!/usr/bin/env python3
+
+import pytest
+import shutil
+import shlex
+import utils
+
+
+@pytest.fixture
+def steps():
+    steps = []
+    return steps
+
+
+@pytest.fixture
+def steps_1(steps):
+    design_file = "test_data/design_ENCSR238SGC_SE.txt"
+    step = [
+        "grep H3K4me1 %s " % (design_file)]
+    return step
+
+
+@pytest.fixture
+def steps_2(steps_1):
+    steps_1.extend([
+        "cut -f7"
+    ])
+    return steps_1
+
+
+def test_run_one_step(steps_1, capsys):
+    check_output = 'ENCSR238SGC\tlimb\tH3K4me1\tNone\t1\tENCSR687ALB\tENCFF833BLU.fastq.gz'.encode('UTF-8')
+    out, err = utils.run_pipe(steps_1)
+    output, errors = capsys.readouterr()
+    assert "first step shlex to stdout" in output
+    assert check_output in out
+
+
+def test_run_two_step(steps_2, capsys):
+    check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'.encode('UTF-8')
+    out, err = utils.run_pipe(steps_2)
+    output, errors = capsys.readouterr()
+    assert "intermediate step 2 shlex to stdout" in output
+    assert check_output in out
+
+
+def test_run_last_step_file(steps_2, capsys, tmpdir):
+    check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'
+    tmp_outfile = tmpdir.join('output.txt')
+    out, err = utils.run_pipe(steps_2, tmp_outfile.strpath)
+    output, errors = capsys.readouterr()
+    assert "last step shlex" in output
+    assert check_output in tmp_outfile.read()