environment-nf-core.yml

# conda env for Nextflow and nf-core testing

# USAGE:
# conda env create -f environment-nf-core.yml -n nf-core
# conda activate nf-core

# NOTE: Make sure you are using the Miniforge distro of conda;
# https://github.com/conda-forge/miniforge

# NOTE: in older versions it was required to run these commands in sequence to get this env to install correctly but this is no longer needed it seems
# Need to run these exact commands to get the env created correctly;  https://bioconda.github.io/#usage
# conda create -y -n nf-core
# conda activate nextflow
# conda config --env --add channels defaults
# conda config --env --add channels bioconda
# conda config --env --add channels conda-forge
# conda config --env --set channel_priority strict
# conda env update --name nf-core --file environment-nf-core.yml

# NOTE: if you have trouble getting it to install, then try removing the nf-core modules

# NOTE: might need to update base conda;
# $ conda update -n base -c defaults conda

# NOTE: alternative way to try installing the env;

# TODO: add nf-test https://code.askimed.com/nf-test/installation/
# $ wget -qO- https://code.askimed.com/install/nf-test | bash

name: nf-core
channels:
  - conda-forge
  - bioconda
dependencies:
  - python>=3.11
  - nextflow>=23.10
  - nf-core>=2.8
  # add some extra items for QoL in various Nextflow demos
  - tower-cli
  - jq
  - yq
  - multiqc