A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I'm trying to launch nf-core/rnaseq on a GCP-backed platform (Verily Workbench) that uses google-batch, and their docs insist that I use containers hosted on <http://gcr.io|gcr.io> rather than nf-core's default <http://quay.io|quay.io>. Is there an existing "mirror" on <http://gcr.io|gcr.io> of all the required containers for nf-core/rnaseq? And if not, does anyone know of a straightforward way to automate copying all the relevant containers from <http://quay.io|quay.io> to <http://gcr.io|gcr.io>?

If you're able to use Seqera's Wave, it has a feature for exactly this: <https://docs.seqera.io/wave/features/mirroring>

Some nf-core pipelines are also set up to be able to configure the base registry if you manually mirror the images yourself, though we are just launching into a new method for defining containers via config files, so this might be a little variable between pipelines now

Note that nf-core doesn't use <http://quay.io|quay.io> exclusively. More and more containers are built using the free Seqera Containers service and are hosted on that domain

Yup: <https://github.com/nf-core/methylseq/blob/4.2.0/assets/genome_target_regions.bed>

This is the file that's used in the automated tests