Hello! I am seeing the following error when testing a pipeline on github actions indicating that the runner is out of space. The pipeline is large and has many dependencies. Any ideas on how to solve this? Thanks!
docker: failed to register layer: write /opt/conda/lib/python3.14/pydoc_data/__pycache__/topics.cpython-314.pyc: no space left on device
https://github.com/nf-core/pathogensurveillance/actions/runs/21022292547/job/60439302804?pr=176
j
James Fellows Yates
01/15/2026, 8:02 AM
You have to find ways to minimise the footprint of the run unfortauntely, in other #C070369GP7T pipelines we've done the following:
• Smaller test data
• Make mini 'mock' databases rather than use full ones
• Split up tests so they start at different points
m
mashehu
01/15/2026, 8:05 PM
There is also a possibility of larger runners...
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Zachary Foster
01/16/2026, 1:55 AM
ok, thanks for the advice! I might try to have it run just a subset of the pipeline. This data set is already so small much of the pipeline is skipped automatically due to lack of data. Is the larger runner something I can configure in
.github
or is that something you have to configure on your end?
Zachary Foster
01/16/2026, 3:32 AM
got it passing by skipping part of the pipeline that wasn't even contributing to the results anyway due to the unrealistically small data subset. Thanks!