Stringtie executables is in PATH variable

[selenaajohn]

I'm trying to use stringtie in my nextflow pipeline and I am getting an error saying:

My issue is that I haven't properly ensured that that the path with newly-built executables is in PATH variable. I have tried adding something to my nextflow conf.ig file, but it hasn't worked. I also tried adding stringtier = "/data/selena/stringtie-2.2.1" to the nextflow config file

nextflow config file:

Nextlow pipeline:

Thanks.

[mribeirodantas]

Do:

env {
  PATH = $PATH:/data/selena/stringtie-2.2.1
}

instead. Or, you can also move the stringtie binary to the .bin/ folder within the project folder of your pipeline. Nextflow will automatically add it to the $PATH of the task. Also, ideally, you should use a container image with the tools you need.

[selenaajohn]

Would that be in the config file or the pipeline?

Thanks for the tip!

[mribeirodantas]

In the nextflow.config file (or any other config file correctly provided, with -c/-C, for example). You're welcome 😄