Very confused about module binaries

[davidmasp]

Hi,

I am trying to include module binaries on my pipeline. Essentially I have a "nextflow module" in a directory with a main.nf script that includes my processes. In addition to that I have a folder in the same directory as resources/usr/bin where I placed a python script with exec. permissions (see below).

nf_base/
├── main.nf
└── resources
    └── usr
        └── bin
            └── plot.py

3 directories, 2 files

From here I try to follow the documentation and include nextflow.enable.moduleBinaries = true in the pipeline. Then I get the error:

ERROR ~ No such variable: moduleBinaries

The same happens both when I include the statement in the pipeline or in the module file. What I am doing wrong?

My nextflow version is: nextflow version 24.04.2.5914

When I remove the statement, then the .command.run file seems to be only loading the PATH for the pipeline directory and not the module bin directory. Am I missing something?

[pditommaso]

This looks like a bug. If you but in the nextflow.config should work. Willing to open an issue?

[davidmasp]

Sure, I ll try generate something easy to reproduce. I have included this in my config file and works as expected, thanks for the tip.

[davidmasp]

Done, see here

#5204