empty SEQUENCE_CONTEXT field

[kubranarci]

Have you checked the docs?

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

Description of the bug

We had a case where SEQUENCE_CONTEXT was empty, which creates a conseqeative problems with createErrorPlots.py and SNVContex_annotator.pl

SEQUENCE_CONTEXT is being extracted in seqContext_annotator.pl

Command used and terminal output

Command executed:

  SNV_context_frequencies.pl \
      snvs_EMQN-RING24-HG38_somatic_snvs_conf_8_to_10.vcf \
      8 > snvs_EMQN-RING24-HG38_snvs_with_context_conf_8_to_10.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NF_SNVCALLING:SNVCALLING:FILTER_SNVS:CONTEXT_FREQUENCIES":
      perl: $(echo $(perl --version 2>&1) | sed 's/.*v\(.*\)) built.*/\1/')
  END_VERSIONS

Command exit status:
  25

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
  SHit with seq context at /omics/odcf/analysis/hipo2_temp/OE0246_emqn_ilc_2024/processing_scripts/nf-snvcalling/bin/SNV_context_frequencies.pl line 59, <FH> line 332.

Work dir:
  /omics/odcf/analysis/hipo2_temp/OE0246_emqn_ilc_2024/processing_scripts/nf-snvcalling/work/f6/e4c4021fb7e10d699072c0948a4827

Relevant files

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System information

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