search

singularityhub / singularity-hpc

Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
https://singularity-hpc.readthedocs.io
Mozilla Public License 2.0
110 stars 25 forks source link

Simple example of Nextflow pipeline using SHPC #479

Open marcodelapierre opened 2 years ago

marcodelapierre commented 2 years ago

Hi @vsoch , I finally had the chance to work on this one today!

Look at this: https://github.com/marcodelapierre/demo-shpc-nf

It's derived from the RNAseq pipeline that the Nextflow authors use as example.

It requires singularity, shpc and modules (documentation to install them not included). The README shows how to run it both with singularity and shpc container modules; in the latter case, the required container installations are shown, too.

I hope it can be useful for you, too, feel free to use,adapt, re-use, ask..!

Marco

vsoch commented 2 years ago

Love this! I'm going to make some time over the weekend to test it out.