Open classic-mcfly opened 3 years ago
Interesting. So your nextflow pipeline would be able to deal with the situation that chloroExtractor
failed due to lack of input data? We could consider terminating because of this reason as a valid outcome with exit status 0. So far I considered it a kind of failure but I see the point in changing it. @greatfireball do you have an opinion on this subject?
We only need to change one character here :smiley: https://github.com/chloroExtractorTeam/chloroExtractor/blob/ce5ffbdd202be9a21c28df576bae1bd8c41f7d88/bin/scale_reads.pl#L383
I already told @MarvinMcFly :)
Nevertheless, due to it changes the behavior, we should both agree to that change. My suggestion would be to add another option (die-without-error-state), which will exit with a code of 0 instead of 1. As default, we are able to still exit with 1
Fine for me
The chloroExtractor terminates with exit status 1 if the input dataset is too small which terminates the whole nextflow pipeline if the errors are not set to be ignored.