miniwdl
miniwdl copied to clipboard
Cannot supply inputs to task only workflows
If a WDL doesn't specify a workflow and only has a task, trying to supply input JSON always errors:
check JSON input; unknown input/output: glob.num_files
Some of the WDL SPEC unit tests depend on this behavior. For example, in this unit test: https://github.com/openwdl/wdl/blob/9c0b9cf4586508a9e6260cc5c5e562e21f625aac/SPEC.md?plain=1#L3776-L3806
version 1.1
task glob {
input {
Int num_files
}
command <<<
for i in 1..~{num_files}; do
printf ${i} > file_${i}.txt
done
>>>
output {
Array[File] outfiles = glob("*.txt")
Int last_file_contents = read_int(outfiles[num_files-1])
}
}
The input to be supplied to the execution engine is "glob.num_files": 3
.
Trying to run that unit test with miniwdl run glob_task.wdl -i '{"glob.num_files": 3}'
returns the same error as above.