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Commit cfdc3a98 authored by Venkat Malladi's avatar Venkat Malladi
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Merge branch '38-fix_bugs' into 'master'

Resolve "Missing modules"

Closes #38

See merge request !32
parents d7b59b36 4dbedfbd
1 merge request!32Resolve "Missing modules"
Pipeline #6620 failed with stages
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...@@ -326,6 +326,8 @@ process crossReads { ...@@ -326,6 +326,8 @@ process crossReads {
} }
else { else {
""" """
module load python/3.6.1-2-anaconda
module load phantompeakqualtools/1.2
python3 $baseDir/scripts/xcor.py -t $seTagAlign python3 $baseDir/scripts/xcor.py -t $seTagAlign
""" """
} }
......
...@@ -24,7 +24,7 @@ def test_upsetplot_singleend(): ...@@ -24,7 +24,7 @@ def test_upsetplot_singleend():
def test_annotation_singleend(): def test_annotation_singleend():
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv' annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
assert os.path.exists(annotation_file) assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 149284 assert utils.count_lines(annotation_file) == 152255
@pytest.mark.pairedend @pytest.mark.pairedend
......
...@@ -11,4 +11,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -11,4 +11,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_software_references(): 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
...@@ -37,7 +37,7 @@ def test_check_update_design(design_diff): ...@@ -37,7 +37,7 @@ def test_check_update_design(design_diff):
def test_overlap_peaks_singleend(): def test_overlap_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak')) assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak' peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
assert utils.count_lines(peak_file) == 149291 assert utils.count_lines(peak_file) == 152262
@pytest.mark.pairedend @pytest.mark.pairedend
......
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