Fix tests.

workflow/tests/test_check_design.py

@@ -6,14 +6,14 @@ from io import StringIO
 import check_design
 
 
-DESIGN_STRING = r"""sample_id\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tfastq_read1
+DESIGN_STRING = """sample_id\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tfastq_read1
 A_1\tA\tLiver\tNone\tNone\t1\tA_1.fastq.gz
 A_2\tA\tLiver\tNone\tNone\t2\tA_2.fastq.gz
 B_1\tB\tLiver\tNone\tNone\t1\tB_1.fastq.gz
-B_2\tB\tLivert\None\tNone\t2\tB_2.fastq.gz
+B_2\tB\tLivert\tNone\tNone\t2\tB_2.fastq.gz
 """
 
-FASTQ_STRING = r"""
+FASTQ_STRING = """
 A_1.fastq.gz\t/path/to/file/A_1.fastq.gz
 A_2.fastq.gz\t/path/to/file/A_2.fastq.gz
 B_1.fastq.gz\t/path/to/file/B_1.fastq.gz
@@ -73,16 +73,18 @@ def fastq_files_1(fastq_files):
 @pytest.mark.unit
 def test_check_headers_singleend(design_1):
     paired = False
+    atac = True
     with pytest.raises(Exception) as excinfo:
-        check_design.check_design_headers(design_1, paired)
+        check_design.check_design_headers(design_1, paired, atac)
     assert str(excinfo.value) == "Missing column headers: ['fastq_read1']"
 
 
 @pytest.mark.unit
 def test_check_headers_pairedend(design):
     paired = True
+    atac = True
     with pytest.raises(Exception) as excinfo:
-        check_design.check_design_headers(design, paired)
+        check_design.check_design_headers(design, paired, atac)
     assert str(excinfo.value) == "Missing column headers: ['fastq_read2']"
 
 

workflow/tests/test_overlap_peaks.py

@@ -10,7 +10,7 @@ import overlap_peaks
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/consensusPeaks/'
 
-DESIGN_STRING = r"""sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate
+DESIGN_STRING = """sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate
 A_1\tA_1.bam\tA_1.bai\tA\tLiver\tNone\tNone\t1
 A_2\tA_2.bam\tA_2.bai\tA\tLiver\tNone\tNone\t2
 B_1\tB_1.bam\tB_1.bai\tB\tLiver\tNone\tNone\t1
@@ -27,8 +27,9 @@ def design_diff():
 
 @pytest.mark.unit
 def test_check_update_design(design_diff):
-    new_design = overlap_peaks.update_design(design_diff)
-    assert new_design.shape[0] == 2
+    atac = True
+    new_design = overlap_peaks.update_design(design_diff, atac)
+    assert new_design.shape[0] == 4
     assert new_design.loc[0, 'peak_caller'] == "bed"
 
 

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -9,7 +9,7 @@ import pool_and_psuedoreplicate
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/design/'
 
-DESIGN_STRING = r"""sample_id\ttag_align\txcor\tbiosample\tfactor\ttreatment\treplicate
+DESIGN_STRING = """sample_id\ttag_align\txcor\tbiosample\tfactor\ttreatment\treplicate
 A_1\tA_1.bedse.gz\tA_1.cc.qc\tLiver\tH3K27ac\tNone\t1
 A_2\tA_2.bedse.gz\tA_2.cc.qc\tLiver\tH3K27ac\tNone\t2
 """
@@ -41,18 +41,6 @@ def test_check_replicates_single(design_experiment_2):
     assert no_reps == 1
 
 
-@pytest.mark.unit
-def test_check_controls(design_experiment):
-    no_controls = pool_and_psuedoreplicate.check_controls(design_experiment)
-    assert no_controls == 2
-
-
-@pytest.mark.unit
-def test_check_controls_single(design_experiment_3):
-    no_controls = pool_and_psuedoreplicate.check_controls(design_experiment_3)
-    assert no_controls == 1
-
-
 @pytest.mark.integration
 def test_pool_and_psuedoreplicate_single_end():
     design_file = os.path.join(test_output_path, 'ENCSR265ZXX_ppr.tsv')

workflow/tests/test_utils.py

@@ -24,14 +24,14 @@ def steps_1(steps):
 @pytest.fixture
 def steps_2(steps_1):
     steps_1.extend([
-        "cut -f8"
+        "cut -f7"
     ])
     return steps_1
 
 
 @pytest.mark.unit
 def test_run_one_step(steps_1, capsys):
-    check_output = 'ENCLB170KFO\tENCSR265ZXX\tA549\tNone\t100nm\tDex\t1\tENCFF115PAE.fastq.gz'.encode('UTF-8')
+    check_output = 'ENCLB170KFO\tENCSR265ZXX\tA549\tNone\t100nm Dex\t1\tENCFF115PAE.fastq.gz'.encode('UTF-8')
     out, err = utils.run_pipe(steps_1)
     output, errors = capsys.readouterr()
     assert "first step shlex to stdout" in output