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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
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Mismatch with new DNAScope ML model format #568

Open Jakob37 opened 2 weeks ago

Jakob37 commented 2 weeks ago

Description of the bug

The Sentieon DNAScope takes a flag --model which is expected to point to a file with a pre-trained model.

In their latest updates, the models are provided in .bundle format. Here the model is accessed as such:

--model /path/to/models.bundle/dnascope.model

(More info in issue here: https://github.com/Sentieon/sentieon-models/issues/4)

But, the file is actually named models.bundle.

So if you point to the models.bundle directly, the Sentieon process does currently not find the file. If pointing directly to dnascope.model, Nextflow will detect it as missing and will not run.

My temporary solution is to update the Sentieon DNA-scope module code as such:

def model_cmd                 = ml_model                           ? " --model ${ml_model}/dnascope.model"   : ''

Command used and terminal output

No response

Relevant files

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System information

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asp8200 commented 2 weeks ago

Yeah, we need to fix that. In the mean time, you can unpack the bundle using ar and get hold of the module-file you need.

EDIT: Your fix is also fine.

Jakob37 commented 2 weeks ago

Yeah, we need to fix that. In the mean time, you can unpack the bundle using ar and get hold of the module-file you need.

EDIT: Your fix is also fine.

Didn't know that, thanks!