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reset vep to 105 #200

Merged
merged 3 commits into from
Sep 25, 2024
Merged

reset vep to 105 #200

merged 3 commits into from
Sep 25, 2024

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nvnieuwk
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@nvnieuwk
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This was causing this error when running VEP with our references:

  MSG: ERROR: gnomAD data is not available in this cache
  
  STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:180
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:122
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:92
  STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
  STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:128
  STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/share/ensembl-vep-112.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:200
  STACK toplevel /usr/local/bin/vep:46
  Date (localtime)    = Wed Sep 25 09:05:51 2024
  Ensembl API version = 112

@nvnieuwk nvnieuwk merged commit 5b0c413 into dev Sep 25, 2024
30 checks passed
@nvnieuwk nvnieuwk deleted the reset-vep-to-105 branch September 25, 2024 12:02
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2 participants