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Commit e3a0a043 authored by Venkat Malladi's avatar Venkat Malladi
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Add in paired end tests for calling peaks.

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......@@ -25,6 +25,6 @@ single_end_mouse:
paired_end_human:
stage: integration
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- nextflow run workflow/main.nf --designFile "/work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
artifacts:
expire_in: 2 days
......@@ -18,5 +18,7 @@ def test_call_peaks_macs_singleend():
@pytest.mark.integration
def test_call_peaks_macs_pairedend():
# Do the same thing for paired end data
pass
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
peak_file = test_output_path + 'ENCLB568IYX_peaks.narrowPeak'
assert utils.count_lines(peak_file) == 112652
......@@ -40,5 +40,7 @@ def test_experiment_design_single_end():
@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
design_file = os.path.join(test_output_path, 'ENCSR729LGA.tsv')
assert os.path.exists(design_file)
design_df = pd.read_csv(design_file, sep="\t")
assert design_df.shape[0] == 2
......@@ -70,5 +70,7 @@ def test_pool_and_psuedoreplicate_single_end():
@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
design_file = os.path.join(test_output_path, 'ENCSR729LGA_ppr.tsv')
assert os.path.exists(design_file)
design_df = pd.read_csv(design_file, sep="\t")
assert design_df.shape[0] == 5
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