Commit 5b44e9ab authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Fix acceptance test to integration tests.

parent 32977563
Pipeline #1561 failed with stages
in 239 minutes and 56 seconds
......@@ -7,7 +7,6 @@ before_script:
stages:
- unit
- integration
- acceptance
user_configuration:
stage: unit
......@@ -18,8 +17,4 @@ single_end_mouse:
stage: integration
script:
- nextflow run workflow/main.nf
single_end_acceptance:
stage: acceptance
script:
- pytest -m acceptance
- pytest -m integration
......@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/callPeaksMACS/'
@pytest.mark.acceptance
@pytest.mark.integration
def test_call_peaks_macs_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
......@@ -16,7 +16,7 @@ def test_call_peaks_macs_singleend():
assert utils.count_lines(peak_file) == 210349
@pytest.mark.acceptance
@pytest.mark.integration
def test_call_peaks_macs_pairedend():
# Do the same thing for paired end data
pass
......@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/convertReads/'
@pytest.mark.acceptance
@pytest.mark.integration
def test_convert_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
......
......@@ -30,7 +30,7 @@ def test_check_update_controls_tag(design_tag):
assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
@pytest.mark.acceptance
@pytest.mark.integration
def test_experiment_design_single_end():
design_file = os.path.join(test_output_path, 'ENCSR238SGC.tsv')
assert os.path.exists(design_file)
......@@ -38,7 +38,7 @@ def test_experiment_design_single_end():
assert design_df.shape[0] == 2
@pytest.mark.acceptance
@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
......@@ -30,7 +30,7 @@ def test_check_update_controls(design_bam):
assert new_design.loc[0, 'control_reads'] == "B_1.bam"
@pytest.mark.acceptance
@pytest.mark.integration
def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
......@@ -38,7 +38,7 @@ def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
@pytest.mark.acceptance
@pytest.mark.integration
def test_experiment_qc_pairedend():
# Do the same thing for paired end data
pass
......@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/filterReads/'
@pytest.mark.acceptance
@pytest.mark.integration
def test_map_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
......@@ -23,6 +23,7 @@ def test_map_qc_singleend():
assert df_library_complexity["PBC2"].iloc[0] == 13.706885
@pytest.mark.integration
def test_map_qc_pairedend():
# Do the same thing for paired end data
pass
......@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/alignReads/'
@pytest.mark.acceptance
@pytest.mark.integration
def test_map_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.srt.bam'))
aligned_reads_report = test_output_path + 'ENCFF646LXU.srt.bam.flagstat.qc'
......@@ -16,7 +16,7 @@ def test_map_reads_singleend():
assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
@pytest.mark.acceptance
@pytest.mark.integration
def test_map_reads_pairedend():
# Do the same thing for paired end data
pass
......@@ -33,14 +33,14 @@ def test_check_update_design(design_diff):
assert new_design.loc[0, 'peak_caller'] == "bed"
@pytest.mark.acceptance
@pytest.mark.integration
def test_overlap_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
assert utils.count_lines(peak_file) == 150302
@pytest.mark.acceptance
@pytest.mark.integration
def test_call_peaks_macs_pairedend():
# Do the same thing for paired end data
pass
......@@ -60,7 +60,7 @@ def test_check_controls_single(design_experiment_3):
assert no_controls == 1
@pytest.mark.acceptance
@pytest.mark.integration
def test_pool_and_psuedoreplicate_single_end():
design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
assert os.path.exists(design_file)
......@@ -68,7 +68,7 @@ def test_pool_and_psuedoreplicate_single_end():
assert design_df.shape[0] == 5
@pytest.mark.acceptance
@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
......@@ -10,7 +10,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.acceptance
@pytest.mark.integration
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
......@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@pytest.mark.acceptance
@pytest.mark.integration
def test_trim_reads_pairedend():
# Do the same thing for paired end data
pass
......@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/crossReads/'
@pytest.mark.acceptance
@pytest.mark.integration
def test_convert_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
......@@ -18,7 +18,7 @@ def test_convert_reads_singleend():
assert df_xcor[9].iloc[0] == 1.266678
@pytest.mark.acceptance
@pytest.mark.integration
def test_map_qc_pairedend():
# Do the same thing for paired end data
pass
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