airrflow

What problem does it solve?

This Skill removes the guesswork from running nf-core/airrflow, helping you analyze immune receptor sequencing data without hunting through docs or inventing flags.

Core Features & Use Cases

• End-to-end AIRR analysis: Supports bulk and single-cell BCR and TCR workflows from raw reads or assembled inputs.
• Reproducible pipeline execution: Uses the pinned release, schema-validated parameters, and provenance capture to keep runs consistent.
• Broad analysis coverage: Handles V(D)J assignment, clonal inference, lineage reconstruction, genotype inference, novel allele detection, RNA-seq extraction, and reporting.
• Practical scenario: Use it to process a TSV samplesheet, run the correct Nextflow command, and produce standardized results and MultiQC reports for a repertoire study.

Quick Start

Ask this skill to run nf-core/airrflow on your TSV samplesheet with the desired profile and output directory, and it will produce the correct invocation, validate the parameters, and preserve reproducibility.