ensembl-vep refseq/merged option broken

[YeHW]

Description of the bug

The code parsing vep related options can't deal with the --refseq/--merged options in the vep command.

If setting:

vep_cache_version: "111"
vep_genome: "GRCh37"
vep_cache: "path/to/vep-cache/"
vep_custom_args: "--refseq --offline --everything"
vep_species: "homo_sapiens_refseq"

then the error is:

  -------------------- EXCEPTION --------------------
  MSG: Should not use homo_sapiens_refseq as --species.
  Try using flags --refseq or --merged with --species homo_sapiens

the command.sh:

vep \
      -i sample.freebayes.vcf.gz \
      -o sample.freebayes_VEP.ann.vcf.gz \
      --stats_file sample.freebayes_VEP.ann.summary.html \
      --vcf --refseq --offline --hgvsg --allele_number --everything --format vcf \
      --compress_output bgzip \
      --fasta human_g1k_v37_decoy.fasta \
      --assembly GRCh37 \
      --species homo_sapiens_refseq \
      --cache \
      --cache_version 111 \
      --dir_cache ${PWD}/ensembl-vep \
      --fork 6

Notice that --species homo_sapiens_refseq is incorrect.
The correct way is to use --species homo_sapiens along with --refseq (latter is present because we include it in vep_custom_args.

The --dir_cache ${PWD}/ensembl-vep (corresponds to vep_cache) is organized as:

${PWD}/ensembl-vep
├── homo_sapiens_refseq
│   ├── 111_GRCh37
│   └── 111_GRCh38
...

which is the default structure if downloaded via ensembl-vep (these files are downloaded via docker myself). For homo_sapiens, there are two more versions, the default homo_sapien and the other one homo_sapiens_merged. If download them all, then the folder would look like:

${PWD}/ensembl-vep
├── homo_sapiens
│   ├── 111_GRCh37
│   └── 111_GRCh38
├── homo_sapiens_merged
│   ├── 111_GRCh37
│   └── 111_GRCh38
├── homo_sapiens_refseq
│   ├── 111_GRCh37
│   └── 111_GRCh38

VEP's annotation folder selection logic:

• By default vep will use ${dir_cache}/${species}/${cache_version}_${assembly}
• If --refseq is provided, it will use ${dir_cache}/${species}_refseq/${cache_version}_${assembly}
• If --merged is provided, it will use ${dir_cache}/${species}_merged/${cache_version}_${assembly}

Below are mappings between vep command options and sarek input params:

• $dir_cache: $vep_cache
• $species: $vep_species
• $cache_version: $vep_cache_version
• $assembly: $vep_genome

However, I'm not sure if this is the case for other species other than homo_sapiens.
For homo_sapiens, the correct logic to parse might be:

• check if vep_custom_args contains --refseq/--merged
• if both not exist, then validate annotation folder existence: ${vep_cache}/${vep_species}/${vep_cache_version}_${vep_genome}
• if any of them exists, should validate annotation folder existence: ${vep_cache}/${vep_species}_refseq/${vep_cache_version}_${vep_genome} or ${vep_cache}/${vep_species}_merged/${vep_cache_version}_${vep_genome} ; note that $vep_species should still be homo_sapiens (because we need --species homo_sapiens in the vep command)

A more consistent way might be to provide another sarek input param to deal with vep's --refseq/--merged option

Command used and terminal output

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Relevant files

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System information

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[YeHW]

This is fixed by #1563