def outputs(self):
return [
ToolOutput(
"out", Stdout(Bam(),
stdoutname=InputSelector("outputFilename"))),
ToolOutput("metrics", File(),
glob=WildcardSelector("metrics.txt")),
]
def outputs(self):
return [
ToolOutput(
"out",
Stdout(Vcf),
doc=
"VCF with length of the variant record added to each record",
)
]
def outputs(self):
return [
ToolOutput("out", Stdout(Bam())),
ToolOutput(
"metrics",
File(),
glob=WildcardSelector("metrics.txt", select_first=True),
),
]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput(
"out", VcfTabix(optional=True), selector=InputSelector("outputFilename")
),
ToolOutput("out_stdout", Stdout(TextFile)),
ToolOutput(
"out_stats",
File(optional=True, extension=".html"),
selector=InputSelector("statsFile"),
),
ToolOutput(
"out_warnings",
File(optional=True, extension=".txt"),
selector=InputSelector("warningFile"),
),
]
def outputs(self):
return [ToolOutput("out", Stdout(Vcf), doc="VCF output")]
def outputs(self):
return [ToolOutput(
"out",
Stdout(Vcf),
doc="Filtered VCF",
)]
def outputs(self) -> List[ToolOutput]:
return [ToolOutput("std", Stdout())]
def outputs(self) -> List[ToolOutput]:
return [ToolOutput("out", Stdout(CompressedVcf()))]
def outputs(self):
return [ToolOutput("out", Stdout(TextFile))]
def outputs(self):
return [
ToolOutput(
"out",
Stdout(Cram(), stdoutname=InputSelector("outputFilename")))
]
def outputs(self):
return [ToolOutput("out", Stdout())]
def test_stdout_normal(self):
s1 = Stdout()
self.assertTrue(True)
import janis_core as j
from janis_core import ToolInput, ToolOutput, Int, Stdout, File
from janis_unix.tools import Echo
AddTwo = j.CommandToolBuilder(
tool="expr",
base_command=None,
arguments=[j.ToolArgument("expr 2 + ", position=0, shell_quote=False)],
version="dev", container="ubuntu:latest",
inputs=[
ToolInput("inp", Int(), position=1)
],
outputs=[
ToolOutput("out", Stdout()),
]
)
w = j.WorkflowBuilder("str_to_int")
w.input("str_input", str)
w.step("echo", Echo(inp=w.str_input))
w.step("exp", AddTwo(inp=w.echo.out.contents().as_int()))
w.output("out", source=w.exp.out)
if __name__ == "__main__":
w.translate("wdl")
def test_recievefromstdout_subtype(self):
s1 = Stdout(FileSubclass())
s2 = File()
self.assertTrue(s2.can_receive_from(s1))
def test_recievefromstdout_optional(self):
s1 = Stdout()
s2 = File(optional=True)
self.assertTrue(s2.can_receive_from(s1))
def test_receivefromstdout_file(self):
s1 = Stdout()
s2 = File()
self.assertTrue(s2.can_receive_from(s1))
def test_receive_from_nonfile_stdout(self):
s1 = FileSubclass()
s2 = Stdout(FileSubclass())
self.assertTrue(s2.can_receive_from(s1))
def test_receivefromstdout_reverse(self):
s1 = File()
s2 = Stdout(FileSubclass())
self.assertFalse(s2.can_receive_from(s1))