Is it not finish doing this?

No, finish allows the currently running jobs to complete. This would tell Nextflow to continue submitting new jobs for as long as it can before dying.

The use case is for automated runs. If there is one bad sample out of hundreds, the run will fail early and need to wait until it can be manually restarted. Then the whole pipeline needs to run through, which is slow. With this option, the other samples would all process so when the pipeline is resumed without the bad sample it would complete very quickly.

yeah, you are right. I was trying to be lazy 😆

We could either change ignore to return a non-zero exit code or add a new strategy like ignoreThenFail, which one would you guys prefer?

I think ignnoreThenFail is the more generally understandable solution.

Agreed.

If you want to be fancy, we could call it defer but I'd like a non-native speaker to check that makes sense.

I generally prefer verbose and clear, for me ignoreThenFail is the winner in this list 👆🏻 defer is more likely to send me scurrying to the docs.

This is the solution that I was looking for. Is it still under consideration ?

I would like to second @boothms message. This would greatly improve the runs with multiple samples where at least one process for one sample might fail. It would be great if the progress of the execution could continue for the rest of the healthy samples.

@bentsherman , thank you so much for jumping on this. I have a quick question about the implementation.

If one sets the errorStrategy 'ignoreThenFail', that implies that the task will never be retried, correct?

Would there be a place where these 2 are not mutually exclusive? Try the maxRetries, and then if it fails, still have the possibility to defer the exit status to the end of the pipeline?

You could do that with a closure:

process.errorStrategy = { task.attempt < 3 ? 'retry' : 'ignoreThenFail' }

This is great. Thank you once again.

I'm really looking forward to testing this.

Hi folks, I saw that the PR is almost done. Do you have an estimate on when this might be merged?

Relevant community discussion: https://community.seqera.io/t/handling-single-sample-failures/618/3