AIRR Seq pipelines

A group of Nextflow workflows and processes for the analysis of AIRR-Seq data from the Adaptive ImmunoSEQ platform and the 10X VDJ platform. The processes mirror the utilities from LymphoSeq2. AIRR Seq pipelines also contain wokrflows for publication specific code. The workflows are designed to run using the module framework on slurm clusters. Future updates will try to make these pipelines more compatible cloud services like AWS or Azure. This repository contains the following workflows:

1. Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy

General requirements

All Nextflow workflows in this repository reuquire at least Nextflow version 20.10.0. The workflows use Nextflow DSL2 syntax. It is configured for slurm clusters and relies on the modules package manager framework for the time being. The following modules are required:

1. Anaconda3
2. Nextflow
3. Singularity
4. R/4.1.0
5. Gliph2

The following R packages are required:

1. tidyverse
2. lubridate
3. devtools
4. readxl
5. optparse
6. LymphoSeq2
7. igraph
8. tidygraph
9. ggraph
10. ggalluvial
11. patchwork
12. scales
13. DT
14. ComplexHeatmap
15. ggpubr
16. circlize
17. viridis

Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy

The workflow for the analysis of T-cell Receptor β-chain repertoires are defined in main.nf under the entry point cfarExperimentOne. A template parameter files is provided here cfar_template.yaml. The required metadata file is provided in the Github repo under metadata/cfar/CFAR_Dean_metadata.xlsx. TRB repertoire sequencing data from the 192 peripheral blood samples is publicly available for access on the Adaptive immunoSEQ Analyzer portal (https://clients.adaptivebiotech.com/pub/towlerton-2022-hiv). The control dataset was sampled from the 786 TRB repertoire sequencing datasets from bone-marrow donors available on the Adaptive immunoSEQ Analyzer portal (Adaptive Biotechnologies, Seattle, WA; https://clients.adaptivebiotech.com/pub/Dean-2015-GenomeMed).

Before running the workflow, please edit the run.sh to specify the following variable:

SCRATCH=/path/to/scratch/directory # Nextflow caches a lot, not specifying a scratch directory will quickly fill up your run directory.

PARAMS=/path/to/params/file.yaml # Please make sure to edit the cfar_template.yaml with the correct paths for all the inputs.

You will also need to edit the nextflow.config with the correct queue name for your slurm configuration.

To run the workflow, run the following command:

./run.sh