errorStrategy advice with exit status > 0

[MaestSi]

Dear all,
I am currently integrating TRF in a NextFlow pipeline. However, with the tool's version I'm currently using "TRF would have a non-zero exit status which was to be interpreted by the user as the number of TRs processed". I tried using errorStrategy = 'ignore', but it seems it is not doing what I would like it to do, as it is not allowing the remaining part of the process to be executed (consisting of other runs of TRF with different parameters). Is there a way I can manage to avoid this issue?
Thanks in advance,
Simone

[bentsherman]

Nextflow used to have a validExitStatus directive that allowed you to specify which exit codes should be considered successful. But that directive was deprecated and removed because I think it had some issues.

The recommended way to handle this kind of problem is to add some bash logic to your process script, such that it returns a 0 exit code at the end. For example:

bash -c 'exit 2' || echo "processed $? TRs"

The first bash command represents a process that returns a non-zero exit code, and I use or (||) to "catch" that exit code, print it, and return 0 exit code like normal.

[MaestSi]

Thank you very much, that worked like a charm!
Simone