Hello, I wonder if there has been any changes in the way that config files are processed? recently, I started to I get the following error running on our HPC using our profile:

Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.

my command:

nextflow run nf-core/rnaseq -r 3.18.0 -resume \

--input samplesheet.csv \

--outdir results \

-profile kaust \

--genome Mus_musculus

The institute profile is recognized and I have the following

includeConfig

statement there that used to get parsed fine until recently:

includeConfig '<https://raw.githubusercontent.com/bioinfo-kaust/references/refs/heads/main/configs/genomes.config>'

any ideas ? thanks a lot!

Same pipelines version? Same Nextflow version?

same pipeline version but the newer Nextflow version (v25.10.5)

Interesting

i just tried with older versions of nextflow but does not work either 😞 so i am not sure what could be the issue

ok, so same pipeline that was working before, with your own set of references has stopped working

now i went back to an old folder and I re-ran the same command but didn't work (unfortunately, have removed the logs and work dir)