Check adequacy of gene IDs between g:Profiler output and downloaded Ensembl annotation

Description of the bug

When running the pipeline with the species aspergillus fumigatus, the tpm normalisation exports an empty dataframe, which results in a bug during the quantile normalisation. This bug is caused by a discrepancy between gene IDs in the count dataframe and the IDs in the downloaded GFF3 file.

It appears that there are two different Ensembl annotations available for aspergillus fumigatus:
https://ftp.ebi.ac.uk/ensemblgenomes/pub/current/fungi/gff3/

The adequacy check should be performed during the step of annotation download, and in case multiple annotations exist, download the one giving the best coverage of gene IDs. In case no annotation provides a sufficient coverage, the pipeline should fail and report a clear error.

Command used and terminal output

nextflow run nf-core/stableexpression -latest -r master -profile apptainer --species aspergillus_fumigatus -resume --outdir results/aspergillus_fumigatus