diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py index e9680f681251d9d9a9db07ce679e5e5d6a0eba2f..5ab6b67cacda1cca075cdbd9e83102eb85b02a2d 100644 --- a/workflow/tests/test_trim_reads.py +++ b/workflow/tests/test_trim_reads.py @@ -3,14 +3,18 @@ import pytest import os +test_data_path = os.path.dirname(os.path.abspath(__file__)) + \ + '/../../test_data/' + +test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ + '/../output/trimReads/' + def test_trim_reads_singleend(): - raw_fastq = os.path.dirname(os.path.abspath(__file__)) + \ - '/../../test_data/ENCFF833BLU.fastq.gz' - trimmed_fastq = os.path.dirname(os.path.abspath(__file__)) + \ - '/../output/trimReads/ENCFF833BLU_trimmed.fq.gz' - trimmed_fastq_report = os.path.dirname(os.path.abspath(__file__)) + \ - '/../output/trimReads/ENCFF833BLU.fastq.gz_trimming_report.txt' + raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz' + trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz' + trimmed_fastq_report = test_output_path + \ + 'ENCFF833BLU.fastq.gz_trimming_report.txt' assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq) assert os.path.getsize(trimmed_fastq) == 2512853101 assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]