resources/usr/bin modules binaries loading not working on Google Cloud

[VasLem]

Bug report

For the following setup:

├── main.nf
├── modules
│   └── download
│       ├── cosmic_annotation.nf
│       ├── resources
│       │   └── usr
│       │       └── bin
│       │           └── read_cosmic.py
│       └── utils.nf
└── nextflow.config

with the main.nf being:

import {download_cosmic} from './modules/download/cosmic_annotation'
workflow {
download_cosmic()
}

and the cosmic_annotation.nf being:

process download_cosmic {
script:
"""
read_cosmic.py
"""
}

the read_cosmic.py file is not found when running on a Google Cloud instance.
The nextflow.config contains the line nextflow.enable.moduleBinaries = true

(Please follow this template replacing the text between parentheses with the requested information)

Expected behavior and actual behavior

The python file to be read and executed, but the file is not found. It is neither in the workdir on the GCS.

Steps to reproduce the problem

./nextflow run main.nf

Program output

(Copy and paste here output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)

/mnt/disks/mybucket/nextflow/64/37bb5b26c9fd3f24f12bd7c0ebfa7e/.command.sh: line 2: ./read_cosmic.py: No such file or directory

Environment

• Nextflow version: 24.03.0-edge

[pditommaso]

Is wave enabled in your config?

[VasLem]

Hi, no. Is this the only supported way to have such a functionality on Google Batch?

[pditommaso]

As per the documentation

This feature requires the use of a local or shared file system for the pipeline work directory, or Wave containers when using cloud-based executors.

[VasLem]

Okay thanks, I will embed the code directly into the process then.