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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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pipestat status flags are not working correctly #463

Closed nsheff closed 3 weeks ago

nsheff commented 4 months ago

If I run a job and it fails, it creates a "_failed.flag", correctly.

When I try to do looper run, it won't run these because they have failed flags -- as expected.

So, I try looper rerun, and what happens is broken. it says:

## [2 of 7] sample: demo1; pipeline: add_to_seqcol
Initialized looper config file: /home/nsheff/code/seqcolapi/analysis/demo/looper_pipestat_config.yaml
Initialize PipestatBackend
Initialize FileBackend
> Skipping sample because rerun requested, but no failed flag found. Status: waiting

That's strange, because there was just a failed flag there, from the previous run... so I double-check and, sure enough, it has changed the flag from failed to waiting!

This doesn't make any sense. It should not change the flag from failed to waiting, and then complain that "no failed flag" is found!

donaldcampbelljr commented 3 months ago

Ok, I found where the issue is; it is due to a fix for https://github.com/pepkit/looper/issues/169, specifically this commit: https://github.com/pepkit/looper/commit/6ccebc65f368e9d5902c3890a0c6373f9e09d169

I've added a fix here: https://github.com/pepkit/looper/pull/480