From 483dd61f1d258d8c547010ba855d3f810e1309bc Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 14 Jan 2019 09:39:24 -0600
Subject: [PATCH] Fix Trim reads output to match.
---
workflow/scripts/trim_reads.py | 6 +++---
workflow/tests/test_trim_reads.py | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index bf5f901..e31ec93 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -76,15 +76,15 @@ def rename_reads(fastq, sample, paired):
if paired: # paired-end data
# Set file names
- renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
- renamed_fastq.append(cwd + '/' + sample + '_R2.fq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R2.fastq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
os.symlink(fastq[1], renamed_fastq[1])
else:
# Set file names
- renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index 5220f18..680f237 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -13,7 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB144FDT_R1.fq.gz'
trimmed_fastq_report = test_output_path + \
'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
@pytest.mark.pairedend
def test_trim_reads_pairedend():
raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_trimmed.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB637LZP_R2.fq.gz'
trimmed_fastq_report = test_output_path + \
- 'ENCLB637LZP_R2_trimmed.fq.gz_trimming_report.txt'
+ 'ENCLB637LZP_R2_val_2.fq.gz_trimming_report.txt'
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]
--
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