Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cannot supply inputs to task only workflows #693

Open
stxue1 opened this issue Jun 19, 2024 · 1 comment
Open

Cannot supply inputs to task only workflows #693

stxue1 opened this issue Jun 19, 2024 · 1 comment
Labels
devex Developers, developers, developers (developer experience) interop Bears on spec compatibility starter new contributors might start here

Comments

@stxue1
Copy link

stxue1 commented Jun 19, 2024

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.

@mlin
Copy link
Collaborator

mlin commented Jun 27, 2024

@stxue1 It should work of you omit the glob. prefix from the input keys. I agree it should tolerate that prefix though.

@mlin mlin added starter new contributors might start here interop Bears on spec compatibility devex Developers, developers, developers (developer experience) labels Jun 27, 2024
@github-project-automation github-project-automation bot moved this to Backlog in miniwdl Aug 28, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
devex Developers, developers, developers (developer experience) interop Bears on spec compatibility starter new contributors might start here
Projects
Status: Backlog
Development

No branches or pull requests

2 participants