RAP and Urgently Needed Nextflow Support

Hi all,

Nextflow has become a central workflow manager in genomics. We, along with other groups, have published several pipelines, such as a GWAS pipeline based on regenie, designed to handle large-scale data from the UK Biobank and similar resources.

Unfortunately, running these pipelines on RAP currently requires starting a cloud workstation and either copying the data or mounting it via FUSE (dxfuse-linux). Both approaches are almost impossible in practice due to the large size of datasets such as imputed data or performance issues with fuse.

Since DNAnexus supports Nextflow via a Nextflow executor, I was wondering if there are plans to make this feature available to RAP users? I think this is urgently needed. Alternatively, is there any recommended way to run Nextflow directly via the CLI within RAP?

For context, there is a previous discussion on this topic here: DNA Nexus and Nextflow on RAP.

Thanks in advance for any guidance!
Sebastian Schönherr