From f1c44814573a33f7d91652daa7b40543090fb5ca Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 19 Aug 2024 11:14:18 -0700 Subject: [PATCH] Fix missing temp_output_dir --- bioluigi/tasks/sratoolkit.py | 1 + tests/test_sratoolkit.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/bioluigi/tasks/sratoolkit.py b/bioluigi/tasks/sratoolkit.py index 58eed0a..514c2c8 100644 --- a/bioluigi/tasks/sratoolkit.py +++ b/bioluigi/tasks/sratoolkit.py @@ -74,6 +74,7 @@ def resources(self): def __init__(self, *kwargs, **kwds): super(FastqDump, self).__init__(*kwargs, **kwds) + self.temp_output_dir = None def program_args(self): args = [cfg.fastqdump_bin, diff --git a/tests/test_sratoolkit.py b/tests/test_sratoolkit.py index 65170d4..b9df022 100644 --- a/tests/test_sratoolkit.py +++ b/tests/test_sratoolkit.py @@ -13,7 +13,7 @@ def test_fastq_dump(): assert '-M' in args assert 18 in args assert args[-3] == '--outdir' - assert args[-2].startswith('outdir-tmp') + assert args[-2] == 'outdir' assert args[-1] == 'srr_accession' assert 'fastq_dump_jobs' in fastq_dump_task.resources assert fastq_dump_task.resources['fastq_dump_jobs'] == 1