brucemoran/nfcore_download_singularity

nf-core tools doesn't download Singularity images properly ATOW

nf-core tools Download Singularity Images

Overview

The nf-core tools download method was not functional when setting up a new workflow on a HPC that is essentially offline. So this repo allows users to download all Singularity images for an nf-core pipeline, along with configs and workflow directories as per nf-core tools download.

Usage

1. Run the command:

   nextflow run brucemoran/nfcore_download_singularity \
    --outdir <path/to/output> \
    --pipeline <nf-core pipeline name> \
    --revision <version> \
    --email me@oh.my
   

2. Output goes to:

   <path/to/output>/<nf-core pipeline name>/<version>/
   

About the output

configs, workflow directories

These directories are the same as is produced by nf-core tools download.

These are output for completeness, and we recommend still be using nextflow pull nf-core/<name> -r <version> to allow running using the standard nextflow run nf-core/<name> -r <version> command syntax.

singularity-images directory

This directory contains .sif images downloaded from depot.galaxy.org and .img images that were pulled from the Docker Hub repo. The latter case happens when no .sif exists for the image.

To use these images it is important to set your $NXF_SINGULARITY_CACHEDIR to the singularity-images directory for the run.