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

[mi3112]

Hi MahShaaban

How do you solve the problem? I'm running VEP through sarek with vep loftee plugin active, and the resulting file doesn't have the annotation. The plugin is present in the image. Into the summary file the code line include the --plugin, but into the vcf resulting file, the plugin flag isn't present.

[MahShaaban]

Hi @mi3112 unfortunately I haven't been able to get the plugin to work. What I've learned since then is that it has to do with the installation of the plugin in the container.