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
--
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