Change default behavior of GatherSampleEvidence to skip running module metrics #633
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# This is due to the interface requirements, as when the default value is true, it requires few other optional arguments to be set. However, this is not clear to a user when running this workflow, and the workflow will fail if the arguments are not provided with less intuitive error messages.
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We have a few workflows like this and I agree it's not ideal.
In this case, however, I think we can change the other parameters. The sv_pipeline_base_docker doesn't exist anymore, so it can be replaced with sv_pipeline_docker, and we can just make primary_contigs_fai required.
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The default input configuration in our template JSONs and Terra workspace includes all inputs required to run module metrics in the workflows where it is enabled by default. I honestly don't think it's a big issue, because we don't expect users to configure inputs from scratch - the inputs are complicated in other ways too. I'm definitely open to disabling module metrics collection by default, and to any changes that improve the clarity of inputs, but I think for now the real solution in terms of ease of use here is to pre-configure the inputs, which we have done. |
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It is a better UX to have the workflows run successfully if only the required input is provided. It seems we can get this covered following Mark's suggestion without changing the default behavior. |
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We should disable module metrics across the pipeline. We don't use them in production and have just been useful for development in a few rare cases. |
The
GatherSampleEvidenceworkflow is set to runGatherSampleEvidenceMetricsby default. However, running that task requires setting values for the optional inputsprimary_contigs_faiandsv_pipeline_base_docker. Therefore, theGatherSampleEvidenceworkflow currently fails if only the required input is provided.Since WDL does not support making the optional inputs as required w.r.t to the value of another argument, and Terra UI lacks features to hint to a user about such a chain of requirements, in-line comments in code seem the only option, as it is implemented. However, in-code comments are less user-friendly and should be reserved for developers and power users only.
Skipping to run this task as a default behavior results in the successful execution of the workflow if only the required input is provided seems to be a better design and improved UX.