vep_sv crashes pipeline if there are no records in output from SVDB merge process

[alkc]

Error executing process > 'vep_sv (SAMPLE_ID_REDACTED)'

Caused by:
  Process `vep_sv (SAMPLE_ID_REDACTED)` terminated with an error exit status (255)

Command executed:

  # Temporary fix for VEP 111.0 annotation bug, where certain MANTA indels are being skipped by VEP
        # See: https://github.com/Ensembl/ensembl-vep/issues/1631#issuecomment-1985973568

        sed 's/SVTYPE=/BAZBAZ=/' SAMPLE_ID_REDACTED.merged.filtered.melt.vcf > SAMPLE_ID_REDACTED.vep111-workaround.vcf

        vep \
                -i SAMPLE_ID_REDACTED.vep111-workaround.vcf \
                -o SAMPLE_ID_REDACTED.vep.vcf \
                --offline \
                --merged \
                --sift b --polyphen b --ccds --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --af --af_1kg --max_af --pubmed --uniprot --mane --tsl --appris --variant_class --gene_phenotype --mirna \
                --synonyms /fs1/resources/ref/hg38//vep/vep111.0/synonyms \
                --vcf \
                --no_stats \
                --fork 10 \
                --force_overwrite \
                --plugin LoFtool \
                --fasta /fs1/resources/ref/hg38//vep/vep111.0/homo_sapiens_merged/111_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
                --dir_cache /fs1/resources/ref/hg38//vep/vep111.0 \
                --dir_plugins /fs1/resources/ref/hg38//vep/vep111.0/Plugins \
                --max_sv_size 50000000 \
                --distance 200 \
                -cache

        # Re-enable SVTYPE:
        sed -i 's/BAZBAZ=/SVTYPE=/' SAMPLE_ID_REDACTED.vep.vcf

  cat <<-END_VERSIONS > vep_sv_versions.yml
  vep_sv:
      vep: $( echo $(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : // ; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  2024-09-17 20:35:22 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this

Command error:
  ERROR: Can't detect input format

Can maybe be worked around by passing --format vcf to vep, but unknown what happens downstreams.