Hi everyone! I need some help with an

nf-core/mag

run. I was running the pipeline on a set of samples, but 4 samples were repeatedly failing during the SPAdes step due to memory limitations. I therefore removed those 4 samples from my samplesheet and tried to restart the pipeline. However, instead of continuing from the completed steps using the existing cache, Nextflow appears to be starting the pipeline from the beginning. I really want to avoid rerunning all the completed steps, as the pipeline has already been running for a long time. What would be the correct way to remove these 4 problematic samples and resume the existing run with only the remaining samples, while retaining the cached results from the previous run? I am using

-resume

, and I have not deleted the

work/

directory. Any advice on the correct approach would be greatly appreciated. Thank you!

Hi! That's strange. Not sure what is breaking the cache there. You can try adding a errorStrategy = 'ignore' to SPAdes, so the fails don't stop the pipeline

Okay, I will try this out! Thanks