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