Commit 6fddf146 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Fix what tests are run and the testing output.

parent d6dd0596
......@@ -12,13 +12,13 @@ user_configuration:
stage: unit
script:
- pytest -m unit
-pytest -m unit --cov=./workflow/scripts
single_end_mouse:
stage: integration
script:
- nextflow run workflow/main.nf -resume
- pytest -m singleend
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
......@@ -27,7 +27,6 @@ paired_end_human:
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- pytest -m pairedend
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
......@@ -36,7 +35,6 @@ single_end_diff:
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
- pytest -m singlediff
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
......@@ -45,6 +43,5 @@ paired_end_diff:
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- pytest -m paireddiff
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
......@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 152840
assert utils.count_lines(annotation_file) == 149820
@pytest.mark.pairedend
......
......@@ -26,7 +26,7 @@ def test_map_qc_singleend():
@pytest.mark.pairedend
def test_map_qc_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bambai'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam.bai'))
filtered_reads_report = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
assert '47389080 + 0 in total' in samtools_report[0]
......
......@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_motif_search_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
peak_file_ENCSR238SGC = test_output_path + 'sorted-ENCSR238SGC.replicated.narrowPeak'
assert os.path.exists(peak_file_ENCSR238SGC)
......@@ -20,7 +20,7 @@ def test_motif_search_singleend():
@pytest.mark.pairedend
def test_motif_search_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html'))
peak_file_ENCSR729LGA= test_output_path + 'sorted-ENCSR729LGA.replicated.narrowPeak'
assert os.path.exists(peak_file_ENCSR729LGA)
......
......@@ -9,20 +9,20 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_map_qc_singleend():
def test_cross_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")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '190,200,210'
assert df_xcor[8].iloc[0] == 1.025906
assert df_xcor[9].iloc[0] == 1.139671
assert round(df_xcor[9].iloc[0], 6) == 1.139671
@pytest.mark.pairedend
def test_map_qc_pairedend():
def test_cross_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '210,220,475'
assert df_xcor[8].iloc[0] == 1.062032
assert round(df_xcor[8].iloc[0],6) == 1.062032
assert df_xcor[9].iloc[0] == 3.737722
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