A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Separate question regarding the same upgrade.
I'm getting
```ERROR nextflow.processor.TaskProcessor - Error executing process &gt; 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE

Command executed:

  tabix -h 2&gt;&amp;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.```
This is running on the ensembl-vep image from quay : `quay/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0`

It used to work fine, but it looks like somewhere along the way the grep command was added / changed (used to be `sed`).
Is there a version of the ensembl image that uses GNU grep and/or should I be running ANNOTATE_MERGE on a different image?

Looks like yes, it changed earlier this year from sed to grep when bumping from VEP 115 to 116.
I'll figure out how i want to handle this separately - not sure I want to change VEP reference version

You should be able to keep the same cache version while bumping the tool without issue

ok thanks; i know ensembl docs recommend keeping them pinned together