No attribute 'MIN_DP'

[marissaDubbelaar]

Description of the bug

The run breaks in the NFCORE_EPITOPEPREDICTION:EPITOPEPREDICTION:PEPTIDE_PREDICTION_VAR step, giving the following error:

Using TensorFlow backend.
  Traceback (most recent call last):
    File "/home-link/kmhmd01/.nextflow/assets/nf-core/epitopeprediction/bin/epaa.py", line 1165, in <module>
      __main__()
    File "/home-link/kmhmd01/.nextflow/assets/nf-core/epitopeprediction/bin/epaa.py", line 994, in __main__
      vl, transcripts, metadata = read_vcf(args.somatic_mutations)
    File "/home-link/kmhmd01/.nextflow/assets/nf-core/epitopeprediction/bin/epaa.py", line 327, in read_vcf
      if isinstance(sample[format_key], list):
    File "/usr/local/lib/python2.7/site-packages/vcf/model.py", line 104, in __getitem__
      return getattr(self.data, key)
  AttributeError: 'CallData' object has no attribute 'MIN_DP'

So I checked what this MIN_DP is in the .vcf file and the header notes the following:

##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum filtered basecall depth used for site genotyping within a non-variant multi-site block">

Command used and terminal output

NXF_VERSION=21.10.4 nextflow run nf-core/epitopeprediction \
--input "" \
--outdir '' \
--genome_version "GRCh38" \
-profile cfc \
-resume

Relevant files

nextflow.log

System information

• Nextflow version: 21.10.4
• Hardware: HPC
• Executor: slurm
• Version of nf-core/epitopeprediction: 2.0.0

[christopher-mohr]

Thanks for reporting. This seems to be caused by "FORMAT properties" that are defined in the header (such as MIN_DP in that case) but are not used in the actual variant content. The problem is that we rely on vcf_reader.formats.keys() which parses all fields given as FORMAT=.