Nextflow/nf-core conda environments and slurm compute environments for seqera platform

Ask for help
1

Hi,

I’m working on setting up a slurm compute environment for my local HPC cluster inside seqera cloud.

One of the requirements is “Nextflow runtime version 22.10.0 (or later) must be pre-installed in the cluster”

When I run nf-core workflows using bash/slurm submission scripts, I activate a conda environment that contains nextflow and nf-core. this environment was created with a command like:

conda create --name nf_env nextflow nf-core

As a result, nextflow (and nf-core) is not installed on my cluster.
Is there a way to use my conda environment in the seqera cloud compute environment setup?
thanks
Charlie

2

I figured out the answer to my question.
During compute environment configuration, I added my module load, and conda activate commands to the:

“staging options → Pre-run script”

section and all went well