Consider the tool with some GenericFile with secondaries [".csv"] (eg: base.txt w/ sec: base.txt.csv:
import janis_core as j
dt = j.GenericFileWithSecondaries(secondaries=[".csv"])
ToolWithSecondaryFiles = j.CommandToolBuilder(
tool="secondary_files",
version="v0.1.0",
container="ubuntu:latest",
base_command="echo",
inputs=[
j.ToolInput("inp", dt, position=0)
],
outputs=[
j.ToolOutput("out", j.Array(dt), selector=j.WildcardSelector("*.txt"))
],
)
This gives the approx WDL translation:
task secondary_files {
input {
File inp
File inp_csv
}
command <<<
set -e
echo ~{inp}
>>>
output {
Array[File] out = glob("*.txt")
# Expect to see
# Array[File] out_csv = ...
}
}
It's missing the output:
Array[File] out_csv = ...
This is probably pretty tricky without a map function in WDL. It might not even be strictly possible. Just thought it be better documented that this is an issue.
Consider the tool with some GenericFile with secondaries
[".csv"](eg:base.txtw/ sec:base.txt.csv:This gives the approx WDL translation:
It's missing the output:
This is probably pretty tricky without a
mapfunction in WDL. It might not even be strictly possible. Just thought it be better documented that this is an issue.