FILTER 'STRANDBIAS' is not defined in the header

[mazzalab]

Description of the bug

NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF fails to read a vcf produced by NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES because the vcf file misses a line in the header.

If, indeed, I edit the vcf file in the temporary directory

by adding a line like:
##FILTER=<ID=STRANDBIAS,Description="Strand bias">

it works

Command used and terminal output

ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (OGM27_R1)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (OGM27_R1)` terminated with an error exit status (255)


Command executed:

  bcftools \
      sort \
      --output OGM27_R1.vcf.gz \
       \
      OGM27_R1_sniffles.vcf

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  Writing to /tmp/bcftools.zGx6RZ
  [W::vcf_parse_filter] FILTER 'STRANDBIAS' is not defined in the header
  Error encountered while parsing the input at chr1:16619298
  Cleaning

Relevant files

No response

System information

No response