Refgenie Nextflow plugin

This plugin links Refgenie and Nextflow. It keeps a Nextflow config file listing all your refgenie-managed assets, so your nextflow pipelines can use them.

Install

pip install git+https://github.com/databio/refgenie_nfcore

Check that refgenie sees it:

refgenie plugins

The nfcore plugin should be listed under the post_update hook with status ok.

Point refgenie to the nextflow config file you want to manage

refgenie plugins set nfcore config_path=/abs/path/to/nextflow.config

This replaces the nextflow_config: key that older refgenie versions read from the refgenie config file.

That's it! Now the file is rewritten after every refgenie command that changes your assets (pull, build, add, remove, rename, and so on). Keep in mind: if using this plugin, your nextflow config file will now be managed by refgenie, so changes you introduce into the file directly will be overwritten by the next refgenie update.

The file has one block per genome alias. Each asset group maps to the path of its default asset:

params {
  genomes {
    'rCRSd' {
      fasta                = "/path/to/genomes/alias/rCRSd/fasta/default/rCRSd.fa"
    }
  }
}

Tutorial

# Set up venv
python3 -m venv env
source env/bin/activate

# Install
pip install refgenie
pip install git+https://github.com/databio/refgenie_nfcore

# Initialize
export REFGENIE_HOME_PATH=`pwd`/refgenie_test
refgenie init
refgenie plugins set nfcore config_path=`pwd`/nextflow.config

# Test
refgenie pull rCRSd/fasta
cat nextflow.config