diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index 6264e3fbf9439669fdd0973228ee4d699077e7ce..bf4528234807779c38123bf02f66af57ce44bc21 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -9,19 +9,19 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_tag_reads_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.tagAlign.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.tagAlign.gz'))
@pytest.mark.singleend
def test_bed_reads_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.bedse.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.bedse.gz'))
@pytest.mark.pairedend
def test_tag_reads_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.tagAlign.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.tagAlign.gz'))
@pytest.mark.pairedend
def test_bed_reads_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.bedpe.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.bedpe.gz'))
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index f91d72b5dc4ef6bc1c4ab0ef620ec3b1a9df37d7..ab94969b9699c204b30df31680fae088cf021c52 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -10,14 +10,14 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_dedup_files_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.bam'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.bam.bai'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.qc'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.bam'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.bam.bai'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.qc'))
@pytest.mark.singleend
def test_map_qc_singleend():
- filtered_reads_report = test_output_path + 'ENCSR238SGC/ENCLB831RUI.dedup.flagstat.qc'
+ filtered_reads_report = test_output_path + 'ENCLB831RUI/ENCLB831RUI.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
assert '64962570 + 0 in total' in samtools_report[0]
assert '64962570 + 0 mapped (100.00%:N/A)' in samtools_report[4]
@@ -25,7 +25,7 @@ def test_map_qc_singleend():
@pytest.mark.singleend
def test_library_complexity_singleend():
- library_complexity = test_output_path + 'ENCSR238SGC/ENCLB831RUI.pbc.qc'
+ library_complexity = test_output_path + 'ENCLB831RUI/ENCLB831RUI.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.926192
assert df_library_complexity["PBC1"].iloc[0] == 0.926775
@@ -34,14 +34,14 @@ def test_library_complexity_singleend():
@pytest.mark.pairedend
def test_dedup_files_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.bam'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.bam.bai'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.qc'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.bam'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.bam.bai'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.qc'))
@pytest.mark.pairedend
def test_map_qc_pairedend():
- filtered_reads_report = test_output_path + 'ENCSR729LGA/ENCLB568IYX.dedup.flagstat.qc'
+ filtered_reads_report = test_output_path + 'ENCLB568IYX/ENCLB568IYX.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
assert '47388510 + 0 in total' in samtools_report[0]
assert '47388510 + 0 mapped (100.00%:N/A)' in samtools_report[4]
@@ -49,7 +49,7 @@ def test_map_qc_pairedend():
@pytest.mark.pairedend
def test_library_complexity_pairedend():
- library_complexity = test_output_path + 'ENCSR729LGA/ENCLB568IYX.pbc.qc'
+ library_complexity = test_output_path + 'ENCLB568IYX/ENCLB568IYX.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.947064
assert round(df_library_complexity["PBC1"].iloc[0],6) == 0.946723
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 9b86193f9d8a98ca05d386c8c81dc291c56b2990..1d64436a1273f82c75929b7ffb468d93c4ae9ec4 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -9,8 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_map_reads_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.bam'))
- aligned_reads_report = test_output_path + 'ENCSR238SGC/ENCLB831RUI.flagstat.qc'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.bam'))
+ aligned_reads_report = test_output_path + 'ENCLB831RUIENCLB831RUI/ENCLB831RUI.flagstat.qc'
samtools_report = open(aligned_reads_report).readlines()
assert '80795025 + 0 in total' in samtools_report[0]
assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
@@ -18,8 +18,8 @@ def test_map_reads_singleend():
@pytest.mark.pairedend
def test_map_reads_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB678IDC.bam'))
- aligned_reads_report = test_output_path + 'ENCSR729LGA/ENCLB678IDC.flagstat.qc'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB678IDC/ENCLB678IDC.bam'))
+ aligned_reads_report = test_output_path + 'ENCLB678IDC/ENCLB678IDC.flagstat.qc'
samtools_report = open(aligned_reads_report).readlines()
assert '72660890 + 0 in total' in samtools_report[0]
assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index b8fdcf4f5f7a7db4cefd33daece9cf25b1ad876c..953f15a3ea65719cdf73a76587cc35459de7397f 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -12,8 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_trim_reads_singleend():
- raw_fastq = test_data_path + 'ENCSR238SGC/ENCFF833BLU.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCSR238SGC/ENCLB144FDT_R1_trimmed.fq.gz'
+ raw_fastq = test_data_path + 'ENCLB144FDT/ENCFF833BLU.fastq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB144FDT/ENCLB144FDT_R1_trimmed.fq.gz'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2512853101
@@ -21,14 +21,14 @@ def test_trim_reads_singleend():
@pytest.mark.singleend
def test_trim_report_singleend():
trimmed_fastq_report = test_output_path + \
- 'ENCSR238SGC/ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
+ 'ENCLB144FDT/ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@pytest.mark.pairedend
def test_trim_reads_pairedend():
- raw_fastq = test_data_path + 'ENCSR729LGA/ENCFF582IOZ.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCSR729LGA/ENCLB637LZP_R2_val_2.fq.gz'
+ raw_fastq = test_data_path + 'ENCLB637LZP/ENCFF582IOZ.fastq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB637LZP/ENCLB637LZP_R2_val_2.fq.gz'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2229312710
@@ -36,5 +36,5 @@ def test_trim_reads_pairedend():
@pytest.mark.pairedend
def test_trim_report_pairedend():
trimmed_fastq_report = test_output_path + \
- 'ENCSR729LGA/ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
+ 'ENCLB637LZP/ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
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 0a79a2c8af77b4cf93b74f6b6ba63265a79c6bbc..fd475943f3f60317c4e0d5dd1ef067cc23fd842d 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -10,12 +10,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_cross_plot_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB144FDT.cc.plot.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT/ENCLB144FDT.cc.plot.pdf'))
@pytest.mark.singleend
def test_cross_qc_singleend():
- qc_file = os.path.join(test_output_path,"ENCSR238SGC/ENCLB144FDT.cc.qc")
+ qc_file = os.path.join(test_output_path,"ENCLB144FDT/ENCLB144FDT.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
@@ -24,12 +24,12 @@ def test_cross_qc_singleend():
@pytest.mark.pairedend
def test_cross_qc_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.cc.plot.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.cc.plot.pdf'))
@pytest.mark.pairedend
def test_cross_plot_pairedend():
- qc_file = os.path.join(test_output_path,"ENCSR729LGA/ENCLB568IYX.cc.qc")
+ qc_file = os.path.join(test_output_path,"ENCLB568IYX/ENCLB568IYX.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '220,430,475'
assert round(df_xcor[8].iloc[0],6) == 1.060018