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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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New --cache option #13

Closed sb10 closed 4 years ago

sb10 commented 4 years ago

Conda and singularity cache defaults to being in the work directory.

When you run the work flow many times, each time with a new work directory, it makes sense to have the cache in a central location and only cache once.

This PR makes it a bit easier to specify the cache location on the command line.

m-bull commented 4 years ago

Thanks!

Worth noting that these should probably be set cluster-wide, and be on some fast network storage:

cat /etc/profile.d/nextflow.sh 
export NXF_CONDA_CACHEDIR=/scratch/${USER}/nextflow/conda-cache
export NXF_SINGULARITY_CACHEDIR=/scratch/${USER}/nextflow/singularity-cache
export NXF_WORK=/scratch/${USER}/nextflow/work