haplotypecaller output unusual behavior without dbsnps/known-sites

[AJTDaedalus]

Description of the bug

When running haplotypecaller without a dbsnps or known-sites parameter (e.g., with non-human organisms) two unusual behaviors occur with the output:

1. If not ran with --skip_step haplotypecaller_filter, the haplotypecaller vcf files are not carried downstream into any further steps like multiqc.
2. If ran with --skip_step haplotypecaller_filter the outputs are carried into multiqc, but are not ran with add_info_to_vcf.

The problem appears to be in the VCF_VARIANT_FILTERING_GATK subworkflow and drops the haplotypecaller output after attempting to call FILTERVARIANTTRANCHES

Command used and terminal output

#1 nextflow run /mnt/storage/data/nf-core-sarek_3.3.2/3_3_2/main.nf --input /mnt/storage/data/samplesheet.csv --outdir /mnt/storage/data/results --fasta /mnt/storage/data/reference/mRatBN7.fa --fasta_fai /mnt/storage/data/reference/mRatBN7.fa.fai --igenomes_ignore --skip_tools baserecalibrator -profile docker --tools deepvariant,freebayes,haplotypecaller

#2 nohup nextflow run /mnt/storage/data/nf-core-sarek_3.3.2/3_3_2/main.nf --input /mnt/storage/data/samplesheet.csv --outdir /mnt/storage/data/results --fasta /mnt/storage/data/reference/mRatBN7.fa --fasta_fai /mnt/storage/data/reference/mRatBN7.fa.fai --igenomes_ignore --skip_tools baserecalibrator,haplotypecaller_filter -profile docker --tools deepvariant,freebayes,haplotypecaller

Relevant files

No response

System information

nextflow v23.10.0.5889
Cloud (32cpu, 512Gb RAM)
Executor (local)
Container: Docker
OS: Ubuntu
Sarek: 3.3.2