nf-core
Is there an way to retrieve a list of download link for all singularity images required, by which I can manually download these images easier.
Description of feature
I can download the pipeline, but singularity images by nf-core download tools. I have to manually download all of singularity images required from “depot.galaxyproject.org/singularity”. It' stime consuming to find the download link in pipelines files. So would you please provide a list of download link for all singularity images required.
Hello Meng,
Normally, you should be able to download the Singularity images together with the pipeline using nf-core pipelines download -s "singularity". So there is not really a need for a manual download of your images.
But if you want to, you can use nextflow inspect on the pipeline. Something along the lines of
nextflow inspect <pipeline> | jq '.processes[].container' | xargs -n 1 singularity pull
should work to get the containers into a local cache directory. This however does not yet fix the problem of naming them in a way that Nextflow will find them easily.
You may have seen that there has been an update to nf-core pipelines download that now wraps nextflow inspect. Please upgrade to tools 3.4.0. I hope this resolves your issues you had with previously downloading the images and saves you the additional work of manual downloads.
Closing this for now, please reopen if you face continued issues.