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CovertLab / vEcoli

Whole cell model of E. coli implemented with Vivarium
https://covertlab.github.io/vEcoli/
MIT License
12 stars 3 forks source link

Must manually check CI output logs for Nextflow failures #240

Closed thalassemia closed 1 month ago

thalassemia commented 1 month ago

Our Nextflow CI workflows are kinda meaningless at the moment because ignored simulation errors do not result in a non-zero exit code for the Nextflow process itself. This feature will be added in Nextflow v24.05.0 via workflow.failOnIgnore. Nextflow v24.05.0 is slated to be the next stable release, so this issue should sort itself out shortly. I do not think it is worth writing custom workflow introspection scripts for this. Instead, users should manually inspect the CI output logs for failures until v24.05.0 is released.

thalassemia commented 1 month ago

Update: The GitHub Action CI job was not properly catching failures because check=True was missing from subprocess.run (fixed in #241). This issue only affects Jenkins CI tests on Sherlock and will be fixed in Nextflow 24.10 (minor versions other than 4 and 10 are only available as edge releases).