exit status when the amount of input data is too small

[classic-mcfly]

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.

[iimog]

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?

[iimog]

We only need to change one character here 😃

chloroExtractor/bin/scale_reads.pl

Line 383 in ce5ffbd

exit 1;

[greatfireball]

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

[iimog]

Fine for me