"nextflow pull nf-core/sarek --help" returned "connection failed" ?

Question

[Glt]

Hi, I am trying to use nextflow and an nf-core pipeline for the first time. I have installed nextflow and nf-core and tried to run this simple command but got the "connection failed" error. I got the same error for a different pipeline such as nf-core/sarek too.

Any suggestion for this?

I am accessing RedHat Linux system of my company remotely and tried to run the below command.

Here is the exact run and error:

$ nextflow run nf-core/sarek --help

N E X T F L O W  ~  version 23.04.2

Pulling nf-core/sarek ...

https://github.com/nf-core/sarek.git: **connection failed**


$ nf-core --version

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.8 - https://nf-co.re


nf-core, version 2.8

Answer 1

[Matthias Zepper]

Most likely, your companies firewall rules do not allow to directly access GitHub? You can download the pipeline first from your laptop and then scp/rsync it on your remote system.

Use nf-core download --container "singularity" -r "3.2.1" sarek to download the pipeline in advance. Include the configs.

[GenoMax]

I have installed nextflow and nf-core

Looks like the software is already installed.

[Phil Ewels]

That's good :) The command suggested downloads the pipeline code from GitHub, along with the singularity images. It doesn't install any software.

[Glt]

Thanks. It looks like you are right. Company has firewall and do not allow to directly access GitHub. If I use the command you shared, how will I be able to catch all the updates? Should I run the same download command each time and upload to the server. Does it have any disadvantage wrt to the default pull command run?

[Phil Ewels]

You'll need to run it again every time you want to use an updated version of the pipeline. So it depends on how often you want to run I guess! :)

It should be equivalent to the nextflow pull command, but with extra stuff (shared nf-core configs and singularity images). Also pulling to a directory instead of NXF_HOME.

Note that if it's _only_ GitHub that doesn't work and the images can be fetched on the fly, you could also just download a zip of the pipeline code from GitHub, transfer expand and run on that.

Answer 2

[GenoMax]

You may need to run off-line (LINK) if you don't have direct internet access (which you probably don't on company server).