How to use Nextflow to call scripts from different environments?
Entering edit mode
12 weeks ago
O.rka ▴ 710

I have the following conda environments:

  • wf-preprocess_env
  • wf-assembly_env

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

  • which I use with wf-preprocess_env environment
  • and 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 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 script and wf [--flags] would call the script both within the bin of wf-assembly_env.

My questions:

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

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

nextflow run --module preprocess -h

Execute a pipeline project
Usage: run [options] Project name or repository url
       Exports all current system environment
       Default: false
anaconda conda nextflow • 517 views
Entering edit mode
12 weeks ago
ATpoint 80k

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

Does this help?

Entering edit mode

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


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