Commit e3e30bf3 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

fix output path in trim pytest

parent f94cd594
Pipeline #7434 failed with stages
in 180 minutes and 5 seconds
......@@ -3,23 +3,22 @@
import pytest
import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
test_output_path = os.path.dirname(os.path.abspath(__file__)) + '/../output/trimReads/'
@pytest.mark.trimData_se
def test_trimData_se():
assert os.path.exists(os.path.join(test_output_path, '/lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/lung2/ENCFF000MDT_hsap__lung_rep2_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver1/ENCFF000MBY_hsap_hepato_rep1_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'lung2/ENCFF000MDT_hsap__lung_rep2_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver1/ENCFF000MBY_hsap_hepato_rep1_trimmed.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed.fq.gz'))
@pytest.mark.trimData_pe
def test_trimData_pe():
assert os.path.exists(os.path.join(test_output_path, '/heart1/heart_a_S2_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/heart1/heart_a_S2_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver2/Liver_b_S2_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver2/Liver_b_S2_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/heart2/heart_b_S4_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/heart2/heart_b_S4_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver1/liver_a_S4_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, '/liver1/liver_a_S4_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'heart1/heart_a_S2_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'heart1/heart_a_S2_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver2/Liver_b_S2_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver2/Liver_b_S2_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'heart2/heart_b_S4_R2_001_val_2.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'heart2/heart_b_S4_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver1/liver_a_S4_R1_001_val_1.fq.gz'))
assert os.path.exists(os.path.join(test_output_path, 'liver1/liver_a_S4_R2_001_val_2.fq.gz'))
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