From e3a0a043e2218a38c935a17e5a907f5547a6e36c Mon Sep 17 00:00:00 2001 From: Venkat Malladi <venkat.malladi@utsouthwestern.edu> Date: Tue, 14 Aug 2018 07:43:05 -0500 Subject: [PATCH] Add in paired end tests for calling peaks. --- .gitlab-ci.yml | 2 +- workflow/tests/test_call_peaks_macs.py | 6 ++++-- workflow/tests/test_experiment_design.py | 6 ++++-- workflow/tests/test_pool_and_psuedoreplicate.py | 6 ++++-- 4 files changed, 13 insertions(+), 7 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index fcde43c..34c0f83 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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 diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py index 6182f24..cba14bf 100644 --- a/workflow/tests/test_call_peaks_macs.py +++ b/workflow/tests/test_call_peaks_macs.py @@ -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 diff --git a/workflow/tests/test_experiment_design.py b/workflow/tests/test_experiment_design.py index 51ada86..1679018 100644 --- a/workflow/tests/test_experiment_design.py +++ b/workflow/tests/test_experiment_design.py @@ -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 diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py index 6c30f7e..ed4bb80 100644 --- a/workflow/tests/test_pool_and_psuedoreplicate.py +++ b/workflow/tests/test_pool_and_psuedoreplicate.py @@ -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 -- GitLab