automatic retrieval of references from genomes_base broken

[mvheetve]

Description of the bug

When running with command:

nextflow -log ${OUTDIR}/.nextflow.log \
	run nf-cmgg/structural -r dev \
	-resume \
	-latest \
	-c /kyukon/scratch/gent/vo/000/gvo00082/vsc43079/structural_WGS/bcftools.config \
	-work-dir ${WORKDIR} \
	--input ${samplesheet} \
	--outdir ${OUTDIR} \
	--genomes_base ${genomes_base} \
	--igenomes_base /kyukon/data/gent/shared/000/gvo00082/genomes \
	--igenomes_ignore true

I receive

Missing `fromPath` parameter -- Check script '.nextflow/assets/nf-cmgg/structural/workflows/structural.nf' at line: 116 or see '/kyukon/data/gent/vo/000/gvo00082/projects/nf-cmgg-structural-filtering/NVQ_457_2026Redo/.nextflow.log' file for more details

line 116 of structural.nf being
def ch_fasta = channel.fromPath(fasta).collect { fasta_file -> [[id:'reference'], fasta_file ] }
Looking at .nextflow.log

Missing `fromPath` parameter -- Check script '.nextflow/assets/nf-cmgg/structural/workflows/structural.nf' at line: 116 or see '/kyukon/data/gent/vo/000/gvo00082/projects/nf-cmgg-structural-filtering/NVQ_457_2026Redo/.nextflow.log' file for more details

full log attached.

When running with

(base) [vsc43079@gligar11 ~]$ nextflow -log ${OUTDIR}/.nextflow.log \
> run nf-cmgg/structural -r dev \
> -resume \
> -latest \
> -c /kyukon/scratch/gent/vo/000/gvo00082/vsc43079/structural_WGS/bcftools.config \
> -work-dir ${WORKDIR} \
> --input ${samplesheet} \
> --outdir ${OUTDIR} \
> --fasta ${fasta} \
> --igenomes_base /kyukon/data/gent/shared/000/gvo00082/genomes \
> --igenomes_ignore true

I receive
Please give the WisecondorX reference using 'wisecondorx_reference'
as expected, so there must be something wrong in the way the references are being retrieved from --genomes_base ${genomes_base}

Command used and terminal output

Relevant files

.nextflow.log

System information

No response