Hello,

I'm trying to write a nextflow script that automates a workflow that will run on a high computing cloud and local computers. The script requires only Bash and Python to be used.

What I'm trying to do is:

1. Load server modules, if it fails because we're on a local computer it just skips that process.

2.Create a conda environment from the yml file that is in the same directory as the nextflow script.

3.Python process in that activated conda environment.

My code: --> This runs in the command line: nextflow run demo_2.nf -with-conda

#!/usr/bin/env nextflow

//process getDirectory{

    """
    // Skip this step for now
    """
//}

process loadModules {

 script:
    """
    echo "Step 1/10 Loading modules if we're on a server - skip if fails"

    ml anaconda3/2023.03 qiime2/2023.5

    echo "Step 2/10 - Creating Conda environment"

    conda env create -f automation_env.yml 

    conda activate automation

    echo "Step 2/10 - Completed"

    """
}


process pythonManifestCreation {
    script:
    """
    #!/usr/bin/env python

    def main():
    # Importing important libraries
        try:
            import pandas as pd
            from pathlib import Path
            import shutil
            import glob
            import os
            print("All necessary modules imported successfully.")
        except ImportError as e:
            print(f"An error occurred while importing modules: {e}")

        main_directory = os.getwd()

output:
path 'r.csv'
}

workflow {

    // Defining the workflow

    loadModules()
    pythonManifestCreation()

}

Here are the errors that I get:

1. If I try to run the script as is, I get an error that conda command not found

Caused by:
  Process loadModules terminated with an error exit status (127)


Command executed:

  echo "Step 2/10 - Creating Conda environment"
  conda env create -f automation_env.yml 
  conda activate automation
  echo "Step 2/10 - Completed"

Command exit status:
  127

Command output:
  Step 2/10 - Creating Conda environment

Command error:
  Step 2/10 - Creating Conda environment
  .command.sh: line 3: conda: command not found

Work dir:
  /home/s/Desktop/nextflow/work/b0/6548e83f5d1fd52282a7828c54075c

2. If I try to run just python script without loading any modules (Because I already have anaconda on my system and the environment is already created! I get this error:

Command exit status:
  127

Command output:
  (empty)

Command error:
  /usr/bin/env: ‘python’: No such file or directory

I have also tried to write a process that captures the directory = \$pwd and pipes it as output: var directory

Everytime I try to pass it into other functions I also get an error for that.

I know this is a very long post, but could someone point me to what I'm doing wrong and how can I approach it better?