If Spades or Bakta fail for small number of samples, is there a way to proceed without these samples?

[masudermann]

Description of the bug

I have encountered this twice, with larger bacterial datasets, but for whatever reason, whether quality of raw read data is bad or spades cannot produce a decent assembly, Bakta will then fail (not surprisingly) and after a few retries, the whole pipeline stops until I remove the samples in question.

Is there a way to proceed with the analysis, even if Spades, or Bakta fail for a small number of samples, making note of which samples couldn't go though the pipeline?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[zachary-foster]

Spades failures will now be ignored and any downstream steps relying on the assembly should be ignored. Feel free to reopen if this is still a problem.