def test_skip_last_node():
tool_1 = Tool(tool_1_def, "T1")
tool_2 = Tool(tool_1_def, "T2")
tool_3 = Tool(tool_1_def, "T3")
p = Pipeline()
node_1 = p.run(tool_1, input='/infile.txt')
node_2 = p.run(tool_2)
node_3 = p.run(tool_3, output='/outfile.txt')
node_1 | node_2 | node_3
groups = list(p.groups())
assert len(groups) == 1
assert node_1._tool.options['input'].get() == '/infile.txt'
assert node_1._tool.options['output'].raw() == sys.stdout
assert node_2._tool.options['input'].raw() == sys.stdout # output of 1
assert node_2._tool.options['output'].raw() == sys.stdout
assert node_3._tool.options['input'].raw() == sys.stdout
assert node_3._tool.options['output'].get() == '/outfile.txt'
p.skip(node_3)
assert len(list(p.nodes())) == 2
assert node_1._tool.options['input'].get() == '/infile.txt'
assert node_1._tool.options['output'].raw() == sys.stdout
assert node_2._tool.options['input'].raw() == sys.stdout
assert node_2._tool.options['output'].get() == '/outfile.txt'
def test_skip_last_node():
tool_1 = Tool(tool_1_def, "T1")
tool_2 = Tool(tool_1_def, "T2")
tool_3 = Tool(tool_1_def, "T3")
p = Pipeline()
node_1 = p.run(tool_1, input='/infile.txt')
node_2 = p.run(tool_2)
node_3 = p.run(tool_3, output='/outfile.txt')
node_1 | node_2 | node_3
groups = list(p.groups())
assert len(groups) == 1
assert node_1._tool.options['input'].get() == '/infile.txt'
assert node_1._tool.options['output'].raw() == sys.stdout
assert node_2._tool.options['input'].raw() == sys.stdout # output of 1
assert node_2._tool.options['output'].raw() == sys.stdout
assert node_3._tool.options['input'].raw() == sys.stdout
assert node_3._tool.options['output'].get() == '/outfile.txt'
p.skip(node_3)
assert len(list(p.nodes())) == 2
assert node_1._tool.options['input'].get() == '/infile.txt'
assert node_1._tool.options['output'].raw() == sys.stdout
assert node_2._tool.options['input'].raw() == sys.stdout
assert node_2._tool.options['output'].get() == '/outfile.txt'
def test_graph_create():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
p.run('nop')
assert len(p._nodes) == 3
assert p.add_edge(a, b) is not None
assert len(p._edges) == 1
def test_graph_create():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
p.run('nop')
assert len(p._nodes) == 3
assert p.add_edge(a, b) is not None
assert len(p._edges) == 1
def test_remove_node():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
c = p.run('nop')
p.add_edge(c, b)
p.add_edge(b, a)
p.remove(b)
assert len(p._nodes) == 2
assert len(p._edges) == 0
for node in p.nodes():
assert len(node._edges) == 0
def test_remove_node():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
c = p.run('nop')
p.add_edge(c, b)
p.add_edge(b, a)
p.remove(b)
assert len(p._nodes) == 2
assert len(p._edges) == 0
for node in p.nodes():
assert len(node._edges) == 0
def test_topological_sort():
p = Pipeline()
a = p.run('nop')
assert a.name == "nop"
b = p.run('nop')
assert a.name == "nop.0"
assert b.name == "nop.1"
c = p.run('nop')
assert a.name == "nop.0"
assert b.name == "nop.1"
assert c.name == "nop.2"
p.add_edge(c, b)
p.add_edge(b, a)
sorted_nodes = [n for n in p.topological_order()]
assert sorted_nodes == [c, b, a]
def test_topological_sort():
p = Pipeline()
a = p.run('nop')
assert a.name == "nop"
b = p.run('nop')
assert a.name == "nop.0"
assert b.name == "nop.1"
c = p.run('nop')
assert a.name == "nop.0"
assert b.name == "nop.1"
assert c.name == "nop.2"
p.add_edge(c, b)
p.add_edge(b, a)
sorted_nodes = [n for n in p.topological_order()]
assert sorted_nodes == [c, b, a]
def test_edge_equality():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
assert p.add_edge(a, b) is not None
assert p.add_edge(a, b) is not None
assert len(p._edges) == 1
def test_edge_equality():
p = Pipeline()
a = p.run('nop')
b = p.run('nop')
assert p.add_edge(a, b) is not None
assert p.add_edge(a, b) is not None
assert len(p._edges) == 1
def test_node_naming_and_auto_indexing_no_names_assigned():
p = Pipeline()
p.run('bash', cmd="ls")
p.run('bash', cmd="ls")
assert p.get("bash.0") is not None
assert p.get("bash.1") is not None
def test_node_naming_and_auto_indexing_no_names_assigned():
p = Pipeline()
p.run('bash', cmd="ls")
p.run('bash', cmd="ls")
assert p.get("bash.0") is not None
assert p.get("bash.1") is not None
outputs = {
"output": None
}
command = """
../tools/quantifier --log DEBUG --annotation ${annotation} -i ${alignment} -o ${output}
"""
if __name__ == "__main__":
pipeline = Pipeline()
# add tools to the pipeline
interleaver = pipeline.add(Interleaver())
aligner = pipeline.add(Aligner())
quantifier = pipeline.add(Quantifier())
# configure the tools
interleaver.reads = "../data/reads_1.fastq ../data/reads_2.fastq"
interleaver.output = "reads.fastq"
aligner.reads = interleaver.output
aligner.index = "../data/genome.gem"
aligner.result = "alignment.map"
quantifier.alignment = aligner.result
quantifier.annotation = "../data/genome.gtf"
quantifier.output = "counts.txt"
pipeline.validate()
pipeline.run()