FILTER column empty and no annotation output

Description of the bug

Hi,

thanks for the code!

I am running Nextflow 25.04.6 and rnavar 1.2.0. The job completes, and in the results dir I see
pipeline_info
preprocessing
reports
samtools
seq2hla
variant_calling

The variant_calling dir reports a .haplotypecaller.combined.g.vcf.gz and .haplotypecaller.combined.g.vcf.gz.tbi for each sample

The FILTER column in the resulting VCFs is empty and the INFO column does not show any VEP annotation, as far as I can see.

Can you please let me know what I am missing ?

Thanks

Command used and terminal output

The command line is as follow
nextflow run nf-core/rnavar  -r 1.2.0 -c $inDIR/loc.config -profile apptainer \
    -work-dir $workDIR \
    --input $inDIR/samplesheet.csv \
    --outdir $outPATH/$outDIR \
    --fasta $GENOME \
    --fasta_fai $GENOMEIDX \
    --gtf $GTF_PATH \
    --read_length 101 \
    --aligner star \
    --star_twopass true \
    --star_index $STAR_INDEX \
    --remove_duplicates false \
    --no_intervals true \
    --generate_gvcf true \
    --known_indels $INDELS \
    --known_indels_tbi $INDELSTBI \
    --dbsnp $DBSNP \
    --dbsnp_tbi $DBSNPTBI \
    --snpeff_db "GRCh38.p13" \
    --tools seq2hla,bcfann,vep \
    --vep_cache $VEPCACHEPATH/.vep \
    --vep_genome "GRCh38" \
    --vep_species "homo_sapiens" \
    --vep_cache_version "110"

Relevant files

No response

System information

No response

Reproduce the supplied Nextflow command and inspect the generated files under variant_calling, especially the combined VCF and its index. Trace the annotation and filtering steps for the listed tools, then confirm that the resulting VCF has populated FILTER and VEP INFO fields.