VCF standardization

[kubranarci]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Running pipeline with hg38 reference with HLA contigs throws issues if there is a mutation. It is related to contig names like:

##contig=<ID=HLA-DRB111:01:01,length=13921>
##contig=<ID=HLA-DRB111:01:02,length=13931>
##contig=<ID=HLA-DRB111:04:01,length=13919>
##contig=<ID=HLA-DRB112:01:01,length=13404>

• and : characters are not acceptable in VCF4.2, so it should be omitted, yet platypus uses the direct IDs from BAM headers.

Find a way to omit this issue when converting nonstandard vcfs into standard VCFs (to avoid issues from tabix and bcftools)

Command used and terminal output

Command executed:

  bcftools sort \
      --output indel_EMQN-RING24-HG38_germline_functional_indels_conf_8_to_10.std.sorted.vcf.gz \
      --temp-dir . \
      --output-type z 
  
  cat <<-END_VERSIONS > versions.yml
  "NF_PLATYPUSINDELCALLING:PLATYPUSINDELCALLING:OUTPUT_STANDARD_VCF:BCFTOOLS_SORT":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Writing to .RoC9Wx
  [E::bcf_hdr_read] Input is not detected as bcf or vcf format
  Could not read VCF/BCF headers from -
  Cleaning

Relevant files

No response

System information

No response