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Added validation section to README.md, error logic if womtool and min…
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…iwdl are disabled
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bshifaw committed Sep 16, 2023
1 parent 3797733 commit 1a37cf7
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7 changes: 7 additions & 0 deletions README.md
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Expand Up @@ -113,6 +113,13 @@ Cromshell is a CLI for submitting workflows to a Cromwell server and monitoring/
* `-c/--color` Color outliers in task level cost results.
* `-d/--detailed` Get the cost for a workflow at the task level.

#### Validate WDL
* `validate <wdl> --dependencies-zip [wdl_zip_file]`
* Validate a WDL file.
* Runs both miniwdl and womtool validation by default, but can be configured to run only one or the other.
* Womtool validation via Cromwell server API does not support validation of imported files, however miniwdl does.
* `--dependencies-zip` MiniWDL option: ZIP file or directory containing workflow source files that are used to resolve local imports.

## Features:
* Running `submit` will create a new folder in the `~/.cromshell/${CROMWELL_URL}/` directory named with the cromwell job id of the newly submitted job.
It will copy your wdl and json inputs into the folder for reproducibility.
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4 changes: 4 additions & 0 deletions src/cromshell/validate/command.py
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Expand Up @@ -80,6 +80,10 @@ def main(

return_code = 0

if no_womtool and no_miniwdl:
LOGGER.error("At least one validation tool must be enabled.")
raise MissingArgumentError("At least one validation tool must be enabled.")

if not no_womtool:
if not wdl_json:
LOGGER.error("WDL JSON file is required.")
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