Hej, I get the following error when I run nf-core/pixelator 2.3.0 using

proxiome-v1-immuno-156-FLAG-v1.1.csv

as panel file:

2026-06-09 20:34:46 [CRITICAL  ]  AssertionError: The following errors were found validating the panel: Panel has missing required columns: {'conj_id'}
  AssertionError: The following errors were found validating the panel: Panel has missing required columns: {'conj_id'}

Samples were prepared with

PIXELGEN PROXIOME KIT IMMUNO 155 v1.1 Proximity Network Assay for Cell Surface Analysis PROXIMM0011 (Lot 2601) spiked with FLAG antibody

, so it should be the correct panel file as far as I understand.

Hi! There has been a few breaking and format changes with the panels lately and it seems you're using one of the newest panels, which is not compatible with nf-core/pixelator 2.3.0. The proper fix would be to update nf-core/pixelator to the latest version (4.1.2), but if this is not possible just now, you could also add a

conj_id

column with dummy values to your panel file. As far as I know this column was here more for backward compatibility reasons.

As @Adrien Coulier said, if you are not able to update to the latest version, another option is to just get the csv file in the right format from an earlier pixelator version (<0.26). https://github.com/PixelgenTechnologies/pixelator/blob/v0.25.0/src/pixelator/pna/resources/panels/proxiome-immuno-156-FLAG-v3.csv

Great, thanks! We will soon do an upgrade to the latest version of the pipeline but at the moment it's difficult for us to keep up with all the updates 🙂