Invalid input reported for vep_plugins.csv

[Stautis]

Description of the bug

Previously, I've run the 0.2.0 version of Nallo, but I figured I'd try running the latest version 0.3.2 as well. I see there are some changes to the vep_plugins.csv file between the two versions so I changed the contents of this file now to match the example given in usage.md for the latest version. However, I'm getting the following warning:

WARN: The following invalid input values have been detected:

* --vep_plugins: /persistent/development/600_wgs_ont_human_rare_disease/input/vep_plugins.csv

And finally, the error which I guess occurs because the invalid input has been ignored:

ERROR ~ No such variable: ch_vep_extra_files

Command used and terminal output

nextflow run ${PIPELINE_URL} -r ${PIPELINE_VERSION} -resume -profile docker -process.executor=slurm -process.queue=low \
                --input ${SAMPLESHEET} \
                --fasta ${REF} --somalier_sites ${SOMALIER_SITES} \
                --par_regions ${PAR_REGIONS} \
                --hificnv_xy ${CNV_XY} --hificnv_xx ${CNV_XX} --hificnv_exclude ${CNV_EX} \
                --trgt_repeats ${TRGT_REPEATS} \
                --variant_catalog ${VARIANT_CATALOG} \
                --vep_cache ${VEP_CACHE} --vep_plugins ${VEP_PLUGINS} --snp_db ${SNP_DB} --variant_consequences_snv ${VAR_CONSEQUENCES} \
                --score_config_snv ${SCORE_SNV} --reduced_penetrance ${REDUCED_PENETRANCE} \
                --preset ONT_R10 --outdir "${OUTPUT_DIR}/${RUN}" --skip_assembly_wf --skip_methylation_wf --skip_repeat_calling false --skip_repeat_annotation false

### Relevant files

[manual-600-385269.log](https://github.com/user-attachments/files/17502859/manual-600-385269.log)
[vep_plugins.csv](https://github.com/user-attachments/files/17502860/vep_plugins.csv)
[nextflow.log](https://github.com/user-attachments/files/17502869/nextflow.log)

### System information

- Nextflow version: 24.04.4
- Hardware: HPC
- Executor: slurm
- Container engine: Docker
- OS: Ubuntu 18.04.6 LTS
- Nallo version: 0.3.2

[fellen31]

Hi, --vep_plugin_files was added in 0.3.0 to separate the VEP plugins from the cache. Perhaps --vep_plugins is a more intuitive name, but for the moment you should use --vep_plugin_files.

All changed, added or removed should be described in the CHANGELOG. There will likely be some more changes to the parameters in the near future, before locking them down.

Hope that helps!

[Stautis]

Yes, that would do it, thanks!