def outputs(self) -> List[j.ToolOutput]:
return [
j.ToolOutput(
"extended",
Csv(),
glob=j.InputSelector("reportPrefix") + ".extended.csv",
),
j.ToolOutput("summary",
Csv(),
glob=j.InputSelector("reportPrefix") +
".summary.csv"),
j.ToolOutput(
"metrics",
j.File(),
glob=j.InputSelector("reportPrefix") + ".metrics.json.gz",
),
j.ToolOutput("vcf",
VcfTabix(),
glob=j.InputSelector("reportPrefix") + ".vcf.gz"),
j.ToolOutput(
"runinfo",
JsonFile(),
glob=j.InputSelector("reportPrefix") + ".runinfo.json",
),
j.ToolOutput(
"rocOut",
j.File(),
glob=j.InputSelector("reportPrefix") + ".roc.all.csv.gz",
),
j.ToolOutput(
"indelLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.INDEL.csv.gz",
),
j.ToolOutput(
"indelPassLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.INDEL.PASS.csv.gz",
),
j.ToolOutput(
"snpLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.SNP.csv.gz",
),
j.ToolOutput(
"snpPassLocations",
j.File(),
glob=j.InputSelector("reportPrefix") +
".roc.Locations.SNP.PASS.csv.gz",
),
]
def convert_javascript_token(self, token: str):
input_selector_match = self.input_selector_matcher.match(token)
if input_selector_match:
return j.InputSelector(input_selector_match.groups()[0])
if token.endswith(".size"):
return j.FileSizeOperator(self.convert_javascript_token(
token[:-5]))
if token.endswith(".basename"):
return j.BasenameOperator(self.convert_javascript_token(
token[:-9]))
if token.endswith(".path"):
# Ignore it because Janis will automatically put this back in where relevant
return self.convert_javascript_token(token[:-5])
if token.endswith(".contents"):
return j.ReadContents(self.convert_javascript_token(token[:-9]))
is_string = self.string_matcher.match(token)
if is_string:
return token[1:-1]
try:
return self.parse_number_from_string(token)
except ValueError:
pass
j.Logger.warn(
f"Couldn't translate javascript token, will use the placeholder '<expr>{token}</expr>'"
)
return f"<expr>{token}</expr>"
def translate_expr(
self,
expr: WDL.Expr.Base,
input_selector_getter: Callable[[str], any] = None
) -> Optional[Union[j.Selector, List[j.Selector], int, str, float, bool]]:
if expr is None:
return None
tp = lambda exp: self.translate_expr(
exp, input_selector_getter=input_selector_getter)
if isinstance(expr, WDL.Expr.Array):
# a literal array
return [self.translate_expr(e) for e in expr.items]
if isinstance(expr, WDL.Expr.String):
return self.translate_wdl_string(expr)
elif isinstance(expr,
(WDL.Expr.Int, WDL.Expr.Boolean, WDL.Expr.Float)):
return expr.literal.value
if isinstance(expr, WDL.Expr.Placeholder):
return self.translate_expr(expr.expr)
if isinstance(expr, WDL.Expr.IfThenElse):
return j.If(tp(expr.condition), tp(expr.consequent),
tp(expr.alternative))
elif isinstance(expr, WDL.Expr.Get):
n = str(expr.expr)
if input_selector_getter:
return input_selector_getter(n)
return j.InputSelector(n)
elif isinstance(expr, WDL.Expr.Apply):
return self.translate_apply(
expr, input_selector_getter=input_selector_getter)
raise Exception(
f"Unsupported WDL expression type: {expr} ({type(expr)})")
def test_1(self):
import janis_core as j
class FileWithSec(j.File):
def __init__(self, optional=False):
super().__init__(optional=optional, extension=".txt")
def secondary_files(self):
return [".sec"]
Tool = j.CommandToolBuilder(
tool="ls",
base_command=["ls"],
inputs=[
j.ToolInput("inp",
FileWithSec,
secondaries_present_as={".sec": "^.sec"})
],
outputs=[
j.ToolOutput("std", j.Stdout),
j.ToolOutput(
"out",
FileWithSec,
secondaries_present_as={".sec": "^.sec"},
glob=j.InputSelector("inp"),
),
],
container="ubuntu:latest",
version="v0.1.0",
)
Tool.translate("wdl")
def get_outputs(self,
names: List[NamedArgument]) -> List[janis.ToolOutput]:
ret = []
for arg in names:
typ = arg.arg.get_type()
if isinstance(typ, cli_types.CliFileSystemType) and typ.output:
ret.append(
janis.ToolOutput(
tag="out_" + arg.name,
output_type=self.arg_to_janis_type(arg.arg),
doc=arg.arg.description,
selector=janis.InputSelector("in_" + arg.name),
))
return ret
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
How to create an empty directory, using the value of an input
"""
import janis_core as j
CLT = j.CommandToolBuilder(
tool="create_initial_stuff",
base_command=["ls", "*"],
version="dev",
container="ubuntu:latest",
inputs=[
j.ToolInput("name_of_output_folder",
j.String(optional=True),
default="some-string")
],
outputs=[j.ToolOutput("out_dir", j.Directory, selector="some-string")],
directories_to_create=[j.InputSelector("name_of_output_folder")],
files_to_create=[(
j.StringFormatter("{dir}/file.txt",
dir=j.InputSelector("name_of_output_folder")),
"contents of file",
)],
)
if __name__ == "__main__":
CLT().translate("cwl")
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
NB: Although WDL supports optional files, some backends of Cromwell do not.
"""
import janis_core as j
ToolWithOptionalOutput = j.CommandToolBuilder(
tool="optional_output_tool",
version="v0.1.0",
container="ubuntu:latest",
base_command=[],
arguments=[j.ToolArgument("echo 1 > ", shell_quote=False)],
inputs=[
j.ToolInput("outputFilename",
j.String(optional=True),
default="out.csv",
position=1)
],
outputs=[
j.ToolOutput("out",
j.File(optional=True),
selector=j.InputSelector("outputFilename"))
],
)
if __name__ == "__main__":
ToolWithOptionalOutput().translate("wdl")
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
We'll use Janis to _try_ and collect a SINGLE file with the extension '.txt',
but one won't exist. CWL will automatically coerce the empty File[0] to File? (null).
However, in WDL, we have do this slightly differently:
File? out = if length(glob("*.txt")) > 0 then glob("*.txt")[0] else None
NB: Although WDL supports optional files, some backends of Cromwell do not.
"""
import janis_core as j
ToolWithDynamicGlob = j.CommandToolBuilder(
tool="tool_with_dynamic_glob",
version="v0.1.0",
container="ubuntu:latest",
base_command=None,
# write '1' to a file called 'out.csv'
arguments=[j.ToolArgument("echo 1 > out.csv", shell_quote=False)],
inputs=[j.ToolInput("extension", str)],
outputs=[
j.ToolOutput("out_csv_files", j.Array(j.File), selector=j.WildcardSelector("*" + j.InputSelector("extension"))),
],
)
if __name__ == "__main__":
ToolWithDynamicGlob().translate("cwl")