Hi everyone, I'm new to the nf-core/airrflow pipeline and had a couple of questions regarding input formats and workflow usage. I noticed that the nf-core/airrflow pipeline (https://nf-co.re/airrflow/4.3.0/docs/usage/usage/single_cell_tutorial/) uses AIRR-formatted files (e.g., Cell Ranger-derived AIRR rearrangement TSVs or raw FASTQs) as input, whereas the official Immcantation tutorials use filtered_contig.fasta and filtered_contig_annotations.csv (https://immcantation.readthedocs.io/en/stable/getting_started/10x_tutorial.html). 1. Why does nf-core/airrflow prefer AIRR-formatted input instead of the formats recommended in Immcantation's own tutorials? Is there an advantage to using AIRR format, or is this a design choice for compatibility or standardization? 2. Should TCR and BCR repertoires be analyzed separately using this pipeline? That is, do I need to run the pipeline once for TCR and once again for BCR? Thanks in advance for your help!

Hi Suchen, all good questions. I think this comes from the fact that initially 10x genomics did not support the AIRR format but now it does so for interoperability with other tools that also support the AIRR format this is now the prefered input format. Immcantation is also transitioning to using the AIRR formatted files.