Singularity pull fails

[ScientistSMC]

Tried to setup Singularity (for offline use) using the instructions in the installation.md file but it failed. See below:

[user]$ singularity pull --name nf-core-rnaseq-1.3.img docker://nf-core/rnaseq:1.3
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/nf-core/rnaseq:1.3
ERROR UNAUTHORIZED: authentication required
ERROR Check existence, naming, and permissions
Cleaning up...
ERROR: pulling container failed!

But I was able to get it working after editing the docker image path to remove the "-" from nf-core based on a similiar issue in another nf-core pipeline (see here: nf-core/chipseq#8). See below:

[user$ singularity pull --name nfcore-rnaseq-1.3.img docker://nfcore/rnaseq:1.3
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/nfcore/rnaseq:1.3
Cache folder set to /home/samcarli/.singularity/docker
[8/8] |===================================| 100.0% 
Importing: base Singularity environment
...

Created a pull request to remove the "-" in the installation.md document.

[apeltzer]

copied my answer from nf-core/rnaseq#311 in here for clarification:

Hey @ScientistSMC !

thank you for submitting your first PR to nf-core/rnaseq. However, we moved the central documentation to our main webpage as downloading Singularity images for offline usage is something not really different across pipelines, which is why we centralized the docs for this.

However, looking up whether this is already correctly stated on our webpage, I just figured out that it's not :-(

See this section over here:

https://nf-co.re/usage/installation#singularity

(which still states the nf-core/YOUR_PIPELINE) and should be docker://nfcore/YOUR_PIPELINE instead.

Looking at the repository of nf-core for the webpage, I found that this looks different in the markdown files we use:

https://github.com/nf-core/nf-co.re/blob/master/markdown/usage/local_installation.md

@ewels I believe this didn't roll out on the webpage as @ScientistSMC found out!

[drpatelh]

@apeltzer @ScientistSMC This indeed needs a fix! See #203

Need to create a PR to the website repo asap now that it's been observed twice in a week! 😅

[apeltzer]

It is a bit weird that the markdown document is already fixed but apparently the webpage didn't update?

https://github.com/nf-core/nf-co.re/blob/master/markdown/usage/local_installation.md#singularity-image

[drpatelh]

Ah, but the bug is in a different page:
https://github.com/nf-core/nf-co.re/blob/master/markdown/usage/installation.md#singularity

[drpatelh]

Fixed in #207