def test_patlas_compiler_channels():
con = [{
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "mash_screen",
"lane": 1
}
}, {
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "mapping_patlas",
"lane": 2
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
nf._set_channels()
nf._set_compiler_channels()
assert len(nf.compilers["patlas_consensus"]["channels"]) == 2
def test_automatic_dependency_multi():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "trimmomatic",
"lane": 1
}
}, {
"input": {
"process": "trimmomatic",
"lane": 1
},
"output": {
"process": "spades",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert len([x for x in nf.processes
if x.template == "integrity_coverage"]) == 1
def test_automatic_dependency_non_raw():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "spades",
"lane": 1
}
}, {
"input": {
"process": "spades",
"lane": 1
},
"output": {
"process": "pilon",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert nf.processes[2].parent_lane == 1
def test_automatic_dependency_wfork_4():
con = [{
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "reads_download",
"lane": 1
}
}, {
"input": {
"process": "reads_download",
"lane": 1
},
"output": {
"process": "skesa",
"lane": 2
}
}, {
"input": {
"process": "reads_download",
"lane": 1
},
"output": {
"process": "spades",
"lane": 3
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
nf._set_channels()
assert nf.processes[4].parent_lane == 3
def test_automatic_dependency_wfork_2():
con = [{
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "spades",
"lane": 1
}
}, {
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "integrity_coverage",
"lane": 2
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
nf._set_channels()
assert len(nf.main_raw_inputs["fastq"]["raw_forks"]) == 2
def test_automatic_dependency_wfork():
con = [{
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "spades",
"lane": 1
}
}, {
"input": {
"process": "__init__",
"lane": 0
},
"output": {
"process": "integrity_coverage",
"lane": 2
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert nf.processes[1].template == "integrity_coverage"
def implicit_link_2():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "spades",
"lane": 1
}
}, {
"input": {
"process": "spades",
"lane": 1
},
"output": {
"process": "assembly_mapping",
"lane": 1
}
}]
return eg.NextflowGenerator(con, "teste.nf", process_map)
def test_extra_inputs_3():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "fastqc={'extra_input':'teste'}",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
nf._set_channels()
assert [list(nf.extra_inputs.keys())[0],
nf.extra_inputs["teste"]["input_type"],
nf.extra_inputs["teste"]["channels"]] == \
["teste", "fastq", ["EXTRA_fastqc_1_2"]]
def test_run_time_directives():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "fastqc={'cpus':'3'}",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert nf.processes[2].directives["fastqc2"]["cpus"] == "3"
def test_invalid_process():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "invalid", "lane": 1}}]
with pytest.raises(SystemExit):
eg.NextflowGenerator(con, "teste.nf")
def test_extra_inputs_invalid_2():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "spades={'extra_input':'teste'}",
"lane": 1
}
}, {
"input": {
"process": "spades",
"lane": 1
},
"output": {
"process": "abricate={'extra_input':'teste'}",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
with pytest.raises(SystemExit):
nf._set_channels()
def test_run_time_directives_full():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "fastqc={'cpus':'3','memory':'4GB',"
"'container':'img','version':'1'}",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert [nf.processes[2].directives["fastqc2"]["cpus"],
nf.processes[2].directives["fastqc2"]["memory"],
nf.processes[2].directives["fastqc2"]["container"],
nf.processes[2].directives["fastqc2"]["version"]] == \
["3", "4GB", "img", "1"]
def test_not_automatic_dependency():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "spades", "lane": 1}}]
with pytest.raises(SystemExit):
eg.NextflowGenerator(con, "teste.nf", auto_dependency=False)
def test_extra_inputs_2():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "integrity_coverage",
"lane": 1
}
}, {
"input": {
"process": "integrity_coverage",
"lane": 1
},
"output": {
"process": "spades",
"lane": 1
}
}, {
"input": {
"process": "spades",
"lane": 1
},
"output": {
"process": "abricate={'extra_input':'teste'}",
"lane": 1
}
}]
nf = eg.NextflowGenerator(con, "teste.nf", process_map)
assert nf.processes[3].extra_input == "teste"
def test_automatic_dependency_2():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "spades", "lane": 1}}]
nf = eg.NextflowGenerator(con, "teste.nf")
assert nf.processes[1].output_channel == nf.processes[2].input_channel
def single_con_multi_raw():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "assembly_mapping", "lane": 1}},
{"input": {"process": "assembly_mapping", "lane": 1},
"output": {"process": "pilon", "lane": 1}}]
return eg.NextflowGenerator(con, "teste.nf")
def test_run_time_directives_invalid():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "fastqc={'cpus'", "lane": 1}}]
with pytest.raises(SystemExit):
eg.NextflowGenerator(con, "teste.nf")
def test_connections_ignore_type():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "skesa", "lane": 1}},
{"input": {"process": "skesa", "lane": 1},
"output": {"process": "patho_typing", "lane": 1}}
]
eg.NextflowGenerator(con, "teste.nf")
def single_con():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "fastqc", "lane": 1}}
]
return eg.NextflowGenerator(con, "teste.nf")
def test_automatic_dependency_3():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "spades", "lane": 1}}]
nf = eg.NextflowGenerator(con, "teste.nf")
assert [nf.processes[1].parent_lane, nf.processes[2].parent_lane] == \
[None, 1]
def test_extra_inputs_1():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "fastqc={'extra_input':'teste'}", "lane": 1}}]
nf = eg.NextflowGenerator(con, "teste.nf")
assert nf.processes[2].extra_input == "teste"
def test_connections_invalid():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "spades", "lane": 1}},
{"input": {"process": "spades", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}}
]
with pytest.raises(SystemExit):
eg.NextflowGenerator(con, "teste.nf")
def test_extra_inputs_invalid():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "fastqc={'extra_input':'default'}", "lane": 1}}]
nf = eg.NextflowGenerator(con, "teste.nf")
with pytest.raises(SystemExit):
nf._set_channels()
def test_patlas_compiler_channels_empty():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "trimmomatic", "lane": 1}}]
nf = eg.NextflowGenerator(con, "teste.nf")
nf._set_channels()
nf._set_compiler_channels()
assert len(nf.compilers["patlas_consensus"]["channels"]) == 0
def raw_forks():
con = [{"input": {"process": "__init__", "lane": 0},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "fastqc", "lane": 1}},
{"input": {"process": "__init__", "lane": 0},
"output": {"process": "patho_typing", "lane": 2}},
{"input": {"process": "__init__", "lane": 0},
"output": {"process": "seq_typing", "lane": 3}}]
return eg.NextflowGenerator(con, "teste.nf")
def test_simple_init():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "{}", "lane": 1}}]
for p in process_map:
con[0]["output"]["process"] = p
nf = eg.NextflowGenerator(con, "teste/teste.nf",
ignore_dependencies=True)
assert [len(nf.processes), nf.processes[1].template] == \
[2, p]
def single_fork():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "spades", "lane": 2}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "skesa", "lane": 3}},
{'input': {'process': 'spades', 'lane': 2},
'output': {'process': 'abricate', 'lane': 2}},
{'input': {'process': 'skesa', 'lane': 3},
'output': {'process': 'abricate', 'lane': 3}}]
return eg.NextflowGenerator(con, "teste.nf")
def single_con_fasta():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "abricate",
"lane": 1
}
}]
return eg.NextflowGenerator(con, "teste.nf", process_map)
def single_status():
con = [{
"input": {
"process": "__init__",
"lane": 1
},
"output": {
"process": "skesa",
"lane": 1
}
}]
return eg.NextflowGenerator(con, "teste.nf", process_map)
def test_extra_inputs_default():
con = [{"input": {"process": "__init__", "lane": 1},
"output": {"process": "integrity_coverage", "lane": 1}},
{"input": {"process": "integrity_coverage", "lane": 1},
"output": {"process": "spades", "lane": 1}},
{"input": {"process": "spades", "lane": 1},
"output": {"process": "abricate={'extra_input':'default'}", "lane": 1}}
]
nf = eg.NextflowGenerator(con, "teste.nf")
nf._set_channels()
assert [list(nf.extra_inputs.keys())[0],
nf.extra_inputs["fasta"]["input_type"],
nf.extra_inputs["fasta"]["channels"]] == \
["fasta", "fasta", ["EXTRA_abricate_1_3"]]
