How to use Nextflow to call scripts from different environments?

Question

[O.rka]

I have the following conda environments:

• wf-preprocess_env
• wf-assembly_env

Each environment has unique dependencies installed. I have 3 scripts:

• preprocess.py which I use with wf-preprocess_env environment
• assembly.py and assembly-long.py which I use with wf-assembly_env

How can I use Nextflow to achieve a similar functionality to this?

wf-wrapper preprocess --flags where wf-wrapper is a wrapper around Nextflow that allows me to have different modules that call different modules.

In the cases listed above,

• wf-wrapper preprocess [--flags] would call the preprocess.py script (and all the dependencies) that are in the bin of wf-preprocess_env. I would also be able to provide it with different --flags such as -h for help or the arguments that are required to run (e.g., -o/--output_directory)
• Similarly, wf assembly [--flags] would call the assembly.py script and wf assembly-long.py [--flags] would call the assembly-long.py script both within the bin of wf-assembly_env.

My questions:

• How can I structure my main.nf Nextflow file to link a module with a specific script and specific environment to load the dependencies?
• Is it possible to wrap the main.nf file (e.g., wf-wrapper.nf) or is the only possibility to use the following notation: nextflow run wf-wrapper.nf --module preprocess [--flags]?

Note: At this point I'm not trying to write an entire pipeline in Nextflow, just to wrap existing scripts in Nextflow so I can easily access the conda environments in the backend.

My current code is the following:

#!/usr/bin/env nextflow

// Define available modules
modules = ['preprocess', 'assembly', 'assembly-long']

// Parse command line options
opts = parseOpts()

// Check if a valid module is provided
if (!opts.module || !(opts.module in modules)) {
    echo "Invalid module. Available modules: ${modules.join(', ')}"
    exit 1
}

// Define the process to execute the specified module
process wrapperScript {
    // Set the Conda environment based on the provided module
    conda "wf-${opts.module}_env"

    // Define the command to run the script with flags
    script:
    """
    # Assuming your scripts are in the bin directory of the Conda environment
    ${opts.module}.py ${opts.flags}
    """
}

// Execute the wrapperScript process
workflow {
    call wrapperScript {
        // Pass module and flags as input parameters
        input:
        module opts.module
        flags opts.flags
    }
}

But when I call Nextflow run it just gives me the Nextflow help:

nextflow run wf-wrapper.nf --module preprocess -h

Execute a pipeline project
Usage: run [options] Project name or repository url
  Options:
    -E
       Exports all current system environment
       Default: false
....

Answer 1

[ATpoint]

You can specify conda environments and containers directly in the modules, see for example:

https://github.com/nf-core/modules/blob/master/modules/nf-core/fastqc/main.nf#L5-L8

Does this help?

[O.rka]

I'm trying to figure out how to make nextflow recognize my $CONDA_PREFIX environment variables. -E doesn't seem to do the trick.