workflow/tests/plot_profile.bats

+#!/opt/bats/libexec/bats-core/ bats
+
+profile_script="./workflow/scripts/plot_profile.sh"
+
+@test "Test deeptools present" {
+  source ${profile_script}
+  run check_tools
+}
+
+@test "Test deeptools computeMatrix" {
+  source ${profile_script}
+  run compute_matrix test_data/ENCSR238SGC_pooled.fc_signal.bw /project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf
+  FILE=computeMatrix.gz
+  if [[ -s "$FILE" ]]; then
+      echo "$FILE exists and not empty"
+  fi
+}
+
+@test "Test deeptools plotProfile" {
+  source ${profile_script}
+  run plot_profile computeMatrix.gz
+  FILE=plotProfile.png
+  if [[ -s "$FILE" ]]; then
+      echo "$FILE exists and not empty"
+  fi
+}

workflow/tests/test_annotate_peaks.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+import utils
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/peakAnnotation/'
+
+
+@pytest.mark.singleend
+def test_pie_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
+
+
+@pytest.mark.singleend
+def test_upsetplot_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
+
+
+@pytest.mark.singleend
+def test_annotation_singleend():
+    annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
+    assert os.path.exists(annotation_file)
+    assert utils.count_lines(annotation_file) >= 149284
+    df = pd.read_csv(annotation_file, sep = "\t", header = 0)
+    print(df.head())
+    #assert df['symbol'].notna().all()
+    assert not(df['symbol'].isnull().values.any())
+
+
+@pytest.mark.pairedend
+def test_pie_pairedend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_pie.pdf'))
+
+
+@pytest.mark.pairedend
+def test_upsetplot_pairedend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
+
+
+@pytest.mark.pairedend
+def test_annotation_pairedend():
+    annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.tsv'
+    assert os.path.exists(annotation_file)
+    assert utils.count_lines(annotation_file) >= 25367
+    df = pd.read_csv(annotation_file, sep = "\t", header = 0)
+    print(df.head())
+    #assert df['symbol'].notna().all()
+    assert not(df['symbol'].isnull().values.any())