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input template generator #654

Merged
merged 15 commits into from
Aug 12, 2023
Merged

input template generator #654

merged 15 commits into from
Aug 12, 2023

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mlin
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@mlin mlin commented Aug 8, 2023

Adds a new subcommand miniwdl input-template to generate a JSON skeleton for the inputs required to run a given WDL. Once filled out, the JSON can then be used with miniwdl run ... -i INPUTS.json.

#553 & builds on work started by @xquek in #639

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mlin commented Aug 8, 2023

@xquek I had some time this past weekend to build on your #639 -- thanks again for getting it started! Key points:

  • I simplified it to templating only the required inputs for now. I need to think about what to put in the template for optional inputs that have defaults, e.g. Int read_length = 150. If it's a constant like that then obviously copy it in, but what if it's some WDL expression with string interpolations etc.? I want to come back to this later but I think the tool is pretty useful even if it's only considering the required inputs.
  • Kept the recursive logic next to the entry point in CLI.py for now. Ultimately I see it moving into the package API as you had it, but keeping it experimental right now while we gain some experience with it and think through the above issue.
  • General polishing & docs

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coveralls commented Aug 8, 2023

Pull Request Test Coverage Report for Build 5793365510

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • 2 unchanged lines in 2 files lost coverage.
  • Overall coverage decreased (-0.03%) to 95.17%

Files with Coverage Reduction New Missed Lines %
WDL/Lint.py 1 98.4%
WDL/runtime/task.py 1 95.96%
Totals Coverage Status
Change from base Build 5643052456: -0.03%
Covered Lines: 7350
Relevant Lines: 7723

💛 - Coveralls

@mlin mlin merged commit c12db6a into main Aug 12, 2023
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3 participants