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Commit de0f2837 authored by Venkat Malladi's avatar Venkat Malladi
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Fix syntax.

parent f0fbf42b
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1 merge request!5Resolve "Add mapping and trimming"
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workflow/tests/test_trim_reads.py
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− 7
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...@@ -2,16 +2,15 @@ ...@@ -2,16 +2,15 @@
import pytest import pytest
import os import os
import gzip
def test_trim_reads_singleend(): def test_trim_reads_singleend():
raw_fastq = os.path.dirname(os.path.abspath(__file__)) + raw_fastq = os.path.dirname(os.path.abspath(__file__)) + \
'../../test_data/ENCFF833BLU_fastq.gz') '../../test_data/ENCFF833BLU_fastq.gz'
trimmed_fastq = os.path.dirname(os.path.abspath(__file__)) + trimmed_fastq = os.path.dirname(os.path.abspath(__file__)) + \
'../output/trimReads/ENCFF833BLU_trimmed.fq.gz') '../output/trimReads/ENCFF833BLU_trimmed.fq.gz'
trimmed_fastq_report = os.path.dirname(os.path.abspath(__file__)) + trimmed_fastq_report = os.path.dirname(os.path.abspath(__file__)) + \
'../output/trimReads/ENCFF833BLU.fastq.gz_trimming_report.txt') '../output/trimReads/ENCFF833BLU.fastq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq) assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2512853101 assert os.path.getsize(trimmed_fastq) == 2512853101
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4] assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
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