Nextflow Stringtie: command not found Error

Question

[selenaajohn]

Im trying to use stringtie in my nextflow pipeline and I've tried to write the stringtie code and have gotten this error. Im not sure how to correct this.

Any help would be greatly appreciated!

[ATpoint]

It's bad practice to delete posts that received an answer ( = a user invested time - in this case me but it of course applies generally). Don't do that again.

Answer 1

[ATpoint]

That's not a Nextflow but a simple bash error. The tool binary is not in PATH. Put the folder with the binary into PATH, or use conda or a container, see Nextflow docs for the latter two.