Python get_args Examples

Example #1

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)

Example #2

def test_list_long():

    sys.argv.append(1)
    args = af.get_args(["build", "-L"])

    with pytest.raises(SystemExit):
        af.build(args)

Example #3

File: test_process_details.py Project: thanhleviet/flowcraft

def test_short_list():

    arguments = af.get_args(["build", "-l"])

    with pytest.raises(SystemExit):
        pd.proc_collector(process_map, arguments)
        

Example #4

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)

Example #5

File: test_assemblerflow.py Project: pedrorvc/flowcraft

def test_build_recipe_innuendo(tmp):

    sys.argv.append(1)
    p = os.path.join(os.path.abspath(tmp), "teste.nf")

    args = af.get_args(
        ["build", "-r", "innuendo", "-o", "{}".format(p), "--pipeline-only"])
    af.build(args)

Example #6

File: test_process_details.py Project: sjackman/flowcraft

def test_long_list():

    arguments = af.get_args(["build", "-L"])

    pipeline_string = "fastqc trimmomatic"

    with pytest.raises(SystemExit):
        pd.proc_collector(process_map, arguments, pipeline_string)

Example #7

File: test_assemblerflow.py Project: saramonzon/flowcraft

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)) == [".treeDag.json", "containers.config",
                                       "lib", "params.config",
                                       "resources.config", "teste.html",
                                       "teste.nf", "user.config"]