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

nf-core

Hello, how to run the nf-core/mag workflow completely offline on a cluster?

You can use `nf-core pipelines download` (<https://nf-co.re/docs/nf-core-tools/cli/pipelines/download|docs>) and then run with `NXF_OFFLINE=true` . You might also have to download some Nextflow plugins manually and put them in `~/.nextflow/plugins` .

See also: <https://nf-co.re/docs/running/run-pipelines-offline>

I followed the guidelines from second link. I am able to get as far as printing the help.

but when I run, it fails

```* The pipeline
    <https://doi.org/10.1093/nargab/lqac007>

* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>

* Software dependencies
    <https://github.com/nf-core/mag/blob/main/CITATIONS.md>

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --igenomes_base (<s3://ngi-igenomes/igenomes/>): could not validate file format of '<s3://ngi-igenomes/igenomes/>': Unable to execute HTTP request: Network is unreachable (SDK Attempt Count: 6)
* --checkm_download_url (<https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz>): the file or directory '<https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz>' does not exist```

You need to unset the options that refer to online files, best to ask for details in <#CE9MS66BS>

If you're not using them in the run, then null should be fine (though I cannot promise since I don't know the pipeline code)

Yes, any (test) data and reference files (e.g. iGenomes) have to exist on a local disk, so you have to download them manually and point the pipeline to them (e.g. with the `--igenomes_base` parameter for reference files or a samplesheet for input data).
For the plugins, the easiest is to run a quick test of the pipeline on a computer connected to the internet (even your laptop).  This will download all plugins, and you can copy the `~/.nextflow/plugins/` over to your offline machine.