Nextflow pipeline to create GO/Phenotypes annotations for pangenomes

[nuno-agostinho]

ENSVAR-5823: GO plugin annotations for pangenomes
ENSVAR-4744: Phenotypes plugin annotations for pangenomes

Steps

This Nextflow pipeline performs the following steps:

1. Download pangenomes data (FASTA and GTF files)
2. Generate GO/Phenotypes plugin annotations for GRCh38
3. Phenotypes only:
   • Filter Phenotypes plugin annotation for 'Genes'
   • Fetch lookup table between gene symbols and Ensembl identifiers from HGNC
4. Create pangenomes annotation (one for each assembly and each plugin):
   • Get the GO/Phenotype info by comparing gene symbols between the GRCh38 and the pangenomes annotation
   • Append info to the pangenome-specific GTFs
5. Test if plugin annotation works for each assembly using VEP

Testing

nextflow run -resume -profile lsf \
  ${ENSEMBL_ROOT_DIR}/ensembl-variation/nextflow/pangenomes \
  $(st1 details script) \
  --version 112

[nakib103]

LGTM!~
thanks Nuno!

[nakib103]

merged to main and release/112