vep_loftee doesn't add the expected columns to INFO/CSQ

[MahShaaban]

Related to #687, which is marked complete but loftee still do not run and generates the same warning.

Description of the bug

I am trying to annotate a vcf file using sarek (3.2.3 or 3.4.2) with --step annotate.

The pipeline starts with the option correctly truned on

Core Nextflow options
  revision.    : 3.4.2
<...>
Annotation
  vep_loftee   : true
  vep_spliceai : true

• vep seems to work fine
• I could use --vep_spliceai fine.
  - Adding --vep_loftee doesn't seem to add any annotations to INFO/CSQ and produces a warning

Command used and terminal output

$ # nextflow run nf-core/sarek -r 3.2.3
$ nextflow run nf-core/sarek -r 3.4.2
-profile singularity
-params-file params.yml
--vep_loftee true
--vep_spliceai true

# The pipeline completes successfully, and I get this warning
WARNING: Failed to compile plugin LoF: Can't locate Bio/Perl.pm in @inc (you may need to inst
all the Bio::Perl module) (@inc contains: /home/mahmed03/.vep/Plugins /usr/local/share/ensemb
l-vep-111.0-0/modules /usr/local/share/ensembl-vep-111.0-0 /usr/local/lib/perl5/5.32/site_per
l /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.32/vendor_perl /usr/local/lib/perl5/v
endor_perl /usr/local/lib/perl5/5.32/core_perl /usr/local/lib/perl5/core_perl .) at /usr/loca
l/share/ensembl-vep-111.0-0/LoF.pm line 46.
BEGIN failed--compilation aborted at /usr/local/share/ensembl-vep-111.0-0/LoF.pm line 46.
Compilation failed in require at (eval 43) line 2.
BEGIN failed--compilation aborted at (eval 43) line 2.

Relevant files

nextflow.log

System information

System information

• Nextflow version: 24.04.4
• Hardware: HPC
• Executor: slurm and local
• Container engine: Singularity
• OS: Linux
• Version of nf-core/sarek: 3.2.3 and 3.4.2

[FriederikeHanssen]

Hm looks like the loftee script is not available in the ensembl container. Are you able to open the container and check if it is available there?

[MahShaaban]

These are the lof files I could find. There isn't a loftee.pm file. But this issue claim that LoFtools should work, meanwhile the issue is Bio:perl not found is the case of the problem

#!/bin/bash

singularity \
    build --sandbox \
    ensembl-vep-111.0 \
    singularity-ensembl-vep-111.0--pl5321h2a3209d_0.img

find ensembl-vep-111.0/ | grep -i lof
#> ensembl-vep-111.0/usr/local/share/ensembl-vep-111.0-0/LoFtool.pm
#> ensembl-vep-111.0/usr/local/share/ensembl-vep-111.0-0/loftee_splice_utils.pl
#> ensembl-vep-111.0/usr/local/share/ensembl-vep-111.0-0/LoF.pm

I noticed that the command output in the .summary is

vep ... --plugins LoF, ...

Not sure if this should be sufficient to invoke loftee/LoFtools