VEPPLUGIN_REVEL fails: grep -oP in the tabix version eval does not work in the bcftools:1.24 container (BusyBox grep)

Description

VEPPLUGIN_REVEL crashes with exit status 2 ("Unable to evaluate output") because the versions_tabix output evaluates

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'

inside the bcftools:1.24--h118bc1c_2 container, whose grep is BusyBox and has no -P. (modules/local/vepplugin/eve/main.nf:15 has the identical line and image; I did not run EVE.)

REVEL is on by default for --genome GRCh38 (plugins are on by default there), so a default GRCh38 run reaches this and the pipeline stops (Pipeline failed).

Where

modules/local/vepplugin/revel/main.nf:15 (dev, commit f590906, PR #212 merge).

Error

ERROR ~ Error executing process > 'INTGENOMICSLAB_LRSOMATIC:LRSOMATIC:PREPARE_VEP_PLUGINS:VEPPLUGIN_REVEL (revel)'

Caused by:
  Unable to evaluate output

Command executed:
  tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'

Command exit status:
  2

Command output:
  grep: invalid option -- 'P'
  BusyBox v1.36.1 (2024-06-02 11:42:27 UTC) multi-call binary.
  Usage: grep [-HhnlLoqvsrRiwFE] [-m N] [-A|B|C N] { PATTERN | -e PATTERN... | -f FILE... } [FILE]...

Reproduce (outside Nextflow)

Both images the module can resolve to behave the same:

# depot.galaxyproject.org singularity image (default branch of the container ternary)
apptainer exec depot.galaxyproject.org-singularity-bcftools-1.24--h118bc1c_2.img \
  sh -c "tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'"
# -> grep: invalid option -- 'P'   (BusyBox v1.36.1)

# docker/quay biocontainer (ext.singularity_pull_docker_container = true branch)
apptainer exec quay.io-biocontainers-bcftools-1.24--h118bc1c_2.img \
  sh -c "tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'"
# -> same error

Suggested fix

Use a portable extraction that works with BusyBox, GNU grep and others. Verified in both images above (prints 1.24):

eval("tabix -h 2>&1 | sed -n 's/^Version: *\\([^ ]*\\).*/\\1/p' | head -n 1")

Applied to the REVEL module in a local clone (and to EVE, untested); with it VEPPLUGIN_REVEL completed (exit 0) and the full pipeline ran to completion (7 PacBio clones, GRCh38). Alternative: awk '/^Version:/{print $2; exit}'.

Environment

• lrsomatic: dev @ f59090672113939acf3b9d36c1bc3584511f3eb8 (2026-10-02)
• Nextflow 26.04.3, Java 17
• Apptainer 1.4.4 (singularity engine), profile vsc_kul_uhasselt,mindwell (KU Leuven VSC)
• --genome GRCh38, VEP plugins left at default (on)

What I did not verify

• Other container engines (Docker, Podman) were not tested; this may only affect images where grep is BusyBox.
• Whether other modules use grep -oP inside minimal images (grep -rn "grep -oP" modules/ also matches modules/nf-core/ensemblvep/vep/main.nf; that process ran fine here, so its image has GNU grep).