From c508559bf4b80849bd2975512681df59d5c247cf Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 27 Dec 2018 08:17:21 -0600
Subject: [PATCH] Fix tests so they run on single end and paired end.
---
.gitlab-ci.yml | 14 ++++++++++----
workflow/tests/test_annotate_peaks.py | 4 ++--
workflow/tests/test_call_peaks_macs.py | 4 ++--
workflow/tests/test_convert_reads.py | 4 ++--
workflow/tests/test_experiment_design.py | 8 ++++----
workflow/tests/test_experiment_qc.py | 4 ++--
workflow/tests/test_map_qc.py | 4 ++--
workflow/tests/test_map_reads.py | 4 ++--
workflow/tests/test_overlap_peaks.py | 4 ++--
workflow/tests/test_pool_and_psuedoreplicate.py | 8 ++++----
workflow/tests/test_trim_reads.py | 5 ++---
workflow/tests/test_xcor.py | 4 ++--
12 files changed, 36 insertions(+), 31 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cc3b607..99d55cb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,7 +17,7 @@ single_end_mouse:
stage: integration
script:
- nextflow run workflow/main.nf -resume
- - pytest -m integration
+ - pytest -m singleend
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
@@ -25,20 +25,26 @@ single_end_mouse:
paired_end_human:
stage: integration
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true
+ - nextflow run workflow/main.nf --designFile "$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
single_end_diff:
stage: integration
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38'
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
+ - pytest -m pairedend
+ - pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
paired_end_diff:
stage: integration
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
+ - pytest -m pairedend
+ - 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 01152c8..2603c36 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -17,7 +17,7 @@ B_2\tB_2.bam\tB_2.bai\tB\tLiver\tH3K27ac\tNone\t2\tB_2
"""
-@pytest.mark.integration
+@pytest.mark.singleend
def test_annotate_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
@@ -27,7 +27,7 @@ def test_annotate_peaks_singleend():
assert utils.count_lines(annotation_file) == 152839
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_annotate_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index cba14bf..a0792c6 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/callPeaksMACS/'
-@pytest.mark.integration
+@pytest.mark.singleend
def test_call_peaks_macs_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
@@ -16,7 +16,7 @@ def test_call_peaks_macs_singleend():
assert utils.count_lines(peak_file) == 210349
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_call_peaks_macs_pairedend():
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'))
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index 52f3fa4..ff8a003 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -7,13 +7,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/convertReads/'
-@pytest.mark.integration
+@pytest.mark.singleend
def test_convert_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
-@pytest.mark.integration
+@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.tagAlign.gz'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bedpe.gz'))
diff --git a/workflow/tests/test_experiment_design.py b/workflow/tests/test_experiment_design.py
index 1679018..3efcca0 100644
--- a/workflow/tests/test_experiment_design.py
+++ b/workflow/tests/test_experiment_design.py
@@ -30,16 +30,16 @@ def test_check_update_controls_tag(design_tag):
assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
-@pytest.mark.integration
-def test_experiment_design_single_end():
+@pytest.mark.singleend
+def test_experiment_design_singleend():
design_file = os.path.join(test_output_path, 'ENCSR238SGC.tsv')
assert os.path.exists(design_file)
design_df = pd.read_csv(design_file, sep="\t")
assert design_df.shape[0] == 2
-@pytest.mark.integration
-def test_experiment_design_paired_end():
+@pytest.mark.pairedend
+def test_experiment_design_pairedend():
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")
diff --git a/workflow/tests/test_experiment_qc.py b/workflow/tests/test_experiment_qc.py
index 308ebe2..5256da5 100644
--- a/workflow/tests/test_experiment_qc.py
+++ b/workflow/tests/test_experiment_qc.py
@@ -30,7 +30,7 @@ def test_check_update_controls(design_bam):
assert new_design.loc[0, 'control_reads'] == "B_1.bam"
-@pytest.mark.integration
+@pytest.mark.singleend
def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
@@ -38,7 +38,7 @@ def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
-@pytest.mark.integration
+@pytest.mark.pairdend
def test_experiment_qc_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index f2c4e74..78e3b39 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/filterReads/'
-@pytest.mark.integration
+@pytest.mark.singleend
def test_map_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
@@ -23,7 +23,7 @@ def test_map_qc_singleend():
assert df_library_complexity["PBC2"].iloc[0] == 13.706885
-@pytest.mark.integration
+@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'))
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 54948bf..3288582 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/alignReads/'
-@pytest.mark.integration
+@pytest.mark.singleend
def test_map_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.srt.bam'))
aligned_reads_report = test_output_path + 'ENCFF646LXU.srt.bam.flagstat.qc'
@@ -16,7 +16,7 @@ def test_map_reads_singleend():
assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_map_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam'))
aligned_reads_report = test_output_path + 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam.flagstat.qc'
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index ce83540..a239b41 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -33,14 +33,14 @@ def test_check_update_design(design_diff):
assert new_design.loc[0, 'peak_caller'] == "bed"
-@pytest.mark.integration
+@pytest.mark.singleend
def test_overlap_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
assert utils.count_lines(peak_file) == 150302
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_overlap_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index ed4bb80..31fffc5 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -60,16 +60,16 @@ def test_check_controls_single(design_experiment_3):
assert no_controls == 1
-@pytest.mark.integration
-def test_pool_and_psuedoreplicate_single_end():
+@pytest.mark.singleend
+def test_pool_and_psuedoreplicate_singleend():
design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
assert os.path.exists(design_file)
design_df = pd.read_csv(design_file, sep="\t")
assert design_df.shape[0] == 5
-@pytest.mark.integration
-def test_experiment_design_paired_end():
+@pytest.mark.pairedend
+def test_experiment_design_pairedend():
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")
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index f759245..b925627 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -10,7 +10,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-@pytest.mark.integration
+@pytest.mark.singleend
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_trim_reads_pairedend():
raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
trimmed_fastq = test_output_path + ' ENCFF582IOZ_val_2.fq.gz'
@@ -30,4 +30,3 @@ def test_trim_reads_pairedend():
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2229312710
assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]
-
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index 87e0304..0c27795 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/crossReads/'
-@pytest.mark.integration
+@pytest.mark.singleend
def test_convert_reads_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")
@@ -18,7 +18,7 @@ def test_convert_reads_singleend():
assert df_xcor[9].iloc[0] == 1.266678
-@pytest.mark.integration
+@pytest.mark.pairedend
def test_map_qc_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")
--
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