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:
- 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?
