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askimed / nf-test

Simple test framework for Nextflow pipelines
https://www.nf-test.com
MIT License
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nf-test with custom plugin gets killed halfway when asserting results #251

Closed AlexVCaron closed 1 month ago

AlexVCaron commented 3 months ago

I'm using a custom plugin with nf-test right now, to capture md5sum from complex data (Nifti-gz, it require a dedicated reader to get consistent md5 from the data inside the file). Nifti being a ND-image format, processing can get quite intensive and RAM can get filled before the Java garbage collector has time to pass.

I was wondeing why my tests tend to get killed halfway. Note I am working in a container and docker enforces resource limits, but I hadn't configured anything that could potentially go over those. Then I discovered the infamous line 54 in the nf-test executable, where there is a -Xmx10g, and I don't have that much RAM. I changed the value to a lower one - 6g in my case - and it works !

Now it's quite a pain to go and change that line everytime the executable changes. Would it be possible to add an option to set that value ? Or default to a standard java way of setting it like the JAVA_TOOL_OPTIONS or something ?

lukfor commented 1 month ago

Thanks. This issue has been fixed in PR #264 and will be available in the next update.

btw: are you interested in listing your nf-test plugin (https://github.com/scilus/nft-nifti) on the plugins page at https://plugins.nf-test.com/?