def test_short_list():
arguments = af.get_args(["build", "-l"])
with pytest.raises(SystemExit):
pd.proc_collector(process_map, arguments)
def test_list_long():
sys.argv.append(1)
args = af.get_args(["build", "-L"])
with pytest.raises(SystemExit):
af.build(args)
def test_check_invalid():
sys.argv.append(1)
args = af.get_args(["build", "-t", "'A B C()'", "-c", "-o teste.nf"])
with pytest.raises(SystemExit):
af.build(args)
def test_check_invalid():
args = af.get_args(["-t 'A B C()'", "-c", "-o teste.nf"])
sys.argv.append(1)
with pytest.raises(SystemExit):
af.run(args)
def test_build_file(tmp):
p = os.path.join(os.path.abspath(tmp), "teste.nf")
sys.argv.append(1)
args = af.get_args(["build", "-t", "integrity_coverage fastqc", "-o",
"{}".format(p)])
af.build(args)
def test_build_file_2(tmp):
p = os.path.join(os.path.abspath(tmp), "teste.nf")
sys.argv.append(1)
args = af.get_args(["-t integrity_coverage fastqc", "-o", "{}".format(p),
"--include-templates"])
af.run(args)
def test_build_file(tmp):
p = os.path.join(os.path.abspath(tmp), "teste.nf")
sys.argv.append(1)
args = af.get_args(["-t integrity_coverage fastqc", "-o", "{}".format(p)])
af.run(args)
assert sorted(os.listdir(tmp)) == ["containers.config", "resources.config",
"teste.html", "teste.nf"]
def test_build_file_2(tmp):
sys.argv.append(1)
p = os.path.join(os.path.abspath(tmp), "teste.nf")
args = af.get_args(["build", "-t integrity_coverage fastqc", "-o",
"{}".format(p), "--pipeline-only"])
af.build(args)
assert sorted(os.listdir(tmp)) == ["containers.config", "lib",
"params.config", "resources.config",
"teste.html", "teste.nf", "user.config"]
def test_list_long():
args = af.get_args(["-L"])
with pytest.raises(SystemExit):
af.run(args)
def test_list_short():
args = af.get_args(["-l"])
with pytest.raises(SystemExit):
af.run(args)