Institutional configs are not included when NXF_OFFLINE is on

[Aratz]

Description of the bug

In the pipeline template, custom_config_base is set so that it will be downloaded from github automatically:

tools/nf_core/pipeline-template/nextflow.config

Line 63 in 34bc338

custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"

As far as I understand, this is the reason this config is excluded later when running in offline mode:

tools/nf_core/pipeline-template/nextflow.config

Line 208 in 34bc338

includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

When downloading institutional profiles, nf-core/tools will set custom_config_base to"${projectDir}/../configs/", but nextflow will still ignore it when NXF_OFFLINE is on.

Either nf-core/tools should remove the conditional on L208 when downloading the institutional profiles, or this conditional should be adapted to include this file as long as custom_config_base does not point to github.

This is a follow up to #3132

How to reproduce:

• nf-core pipelines download demultiplex --download-configuration yes --compress none --revision 1.5.4 --container-system singularity
• export NXF_OFFLINE='true'
• nextflow run nf-core-demultiplex_1.5.4/1_5_4/main.nf -profile test,singularity,uppmax --outdir outdir

Command used and terminal output

N E X T F L O W   ~  version 24.10.3

Unknown configuration profile: 'uppmax'

System information

No response

[MatthiasZepper]

I think, the problem is simply a wrong negation for !System.getenv('NXF_OFFLINE'), because the intention was to enable the local configs only when the system is offline.

As of now, the evaluation looks like this:

NXF_OFFLINE	params.custom_config_base	Result
Set (true)	Set (true)	"/dev/null"
Set (true)	Not set (false/null)	"/dev/null"
Not set (false/null)	Set (true)	"${params.custom_config_base}/nfcore_custom.config"
Not set (false/null)	Not set (false/null)	"/dev/null"

But even if I do not set NXF_OFFLINE (we anyway do not set it, because it causes other issues), it does not work in Seqera Platform.

[Aratz]

I'm not sure I follow, wouldn't one want to be able to use the institutional configs regardless if one is online or not?

Essentially, the default behavior to download the institutional configs from https://github.com/nf-core/configs/. If users want to use them offline, they should set params.custom_config_base to the actual location where they downloaded the files, and if they don't want these file they should set params.custom_config_base to null.

Don't we want the truth table to look something like this instead?

NXF_OFFLINE	params.custom_config_base	Result
Set (true)	Set (true)	"${params.custom_config_base}/nfcore_custom.config" *
Set (true)	Not set (false/null)	"/dev/null"
Not set (false/null)	Set (true)	"${params.custom_config_base}/nfcore_custom.config"
Not set (false/null)	Not set (false/null)	"/dev/null"

* Assuming the users have set params.custom_config_base to a local path

Namely the conditional would be independent of NXF_OFFLINE as @bentsherman initially suggested and would look something like:

includeConfig params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : '/dev/null'

[bentsherman]

Good point. The institutional configs should be included even in offline mode, if they are locally available. So something like:

includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

You could also just condition on params.custom_config_base != null but I think they didn't go for that because then offline users would have to remember to set the option to null

@MatthiasZepper we fixed that issue in platform but I don't know if it was backported, so depending on your version you might not have the fix yet