Hi @Gisela Gabernet, thanks for all your help so far! AIRRflow has been really helpful for our analysis. I'm wondering now about whether there are parameters within AIRRflow I can use that will allow us to run Dowser to load in the light chain sequence for building phylogenetic trees based on both H+L chains? I know that you've mentioned before that the clonal analysis is done taking into account splitting clonal groups on the light chain as well. I've noticed after looking carefully at the formatted_clones.RDS that only the sequences for the heavy chain have been loaded in (lsequence field is empty), and I think this has to do with how formatClones is run (see the screenshot of the subject_x_dowser_report' index.html). Are there any parameters in AIRRflow to allow run the phylogenetic tree building with heavy and light chain sequences? The AIRRflow command I ran was:

nextflow run nf-core/airrflow -r 4.1.0 -profile biowulf --input Ainhoa_BCR_SampleSheet.tsv --mode assembled  --outdir Jun132024run_AinhoaBCR_results_igphyml --cloneby subject_id --lineage_trees --lineage_tree_builder igphyml --lineage_tree_exec /data/homc/igphyml/src/igphyml

Hi @Margaret Ho, sorry for the late reply. Unfortunately at the moment it is not possible to build lineage trees according to both heavy and light chains within airrflow, but that is something we would like to implement soon. Meanwhile, here is a tutorial on how to do that with Dowser directly: https://dowser.readthedocs.io/en/latest/vignettes/Resolve-Light-Chains-Vignette/ You can depart from the clones already defined by airrflow. Let me know if you have any issues in running the tutorial and I will put you in contact with the Dowser developers.

Thank you for the reply!