From 6fddf14634839c91ac91a70cc383565fe4b6e5af Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 7 Jan 2019 07:15:16 -0600
Subject: [PATCH] Fix what tests are run and the testing output.
---
.gitlab-ci.yml | 5 +----
workflow/tests/test_annotate_peaks.py | 2 +-
workflow/tests/test_map_qc.py | 2 +-
workflow/tests/test_motif_search.py | 4 ++--
workflow/tests/test_xcor.py | 8 ++++----
5 files changed, 9 insertions(+), 12 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 60a430b..93373d2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index e3f5746..1381350 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -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
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 78e3b39..95841df 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -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]
diff --git a/workflow/tests/test_motif_search.py b/workflow/tests/test_motif_search.py
index 577407a..ca84f4a 100644
--- a/workflow/tests/test_motif_search.py
+++ b/workflow/tests/test_motif_search.py
@@ -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)
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index 8492de4..2d3fdcf 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -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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