Hi,

I am attempting to use an existing conda environment in a nextflow script (I do not want to point to a .yml file and compile environments). I have followed the instructions suggested by nextflow for using an existing environment:

process foo {
conda '/path/to/an/existing/env/directory'

'''
your_command --here
'''
}

Here is my attempt:

#!/usr/bin/env nextflow

process foo {
echo true
conda '/home/barry/anaconda3/envs/circexplorer2'

script:
"""
CIRCexplorer2 --help
"""
}

It gives the folowing error, pointing to the .command.run line 77:

.command.run: line 77: activate: No such file or directory

Looking at the file:

# conda environment
source activate /home/barry/anaconda3/envs/circexplorer2

It seems strange that it is using the depreciated source activate call, but maybe I'm missing a trick. Any thoughts?

p.s I have stripped the path and provided conda 'circexplorer2' to the nextflow script, but it tries to create the environment which is not the behaviour I was hoping for.

Regards,

Barry