TronFlow HLA typing pipeline
Nextflow (Di Tommaso, 2017) pipeline for HLA typing using HLA-HD (Kawaguchi, 2017).
How to run it
Prepare an input table with the FASTQs for each sample with three tab-separated columns without a header
| Sample name | FASTQ1 | FASTQ2 |
|---|---|---|
| sample_1 | /path/to/sample_1.1.fq | /path/to/sample_1.2.fq |
| sample_2 | /path/to/sample_2.1.fq | /path/to/sample_2.2.fq |
Run as indicated below.
$ nextflow run tron-bioinformatics/tronflow-hla-hd --help
N E X T F L O W ~ version 19.07.0
Launching `main.nf` [intergalactic_shannon] - revision: e707c77d7b
Usage:
nextflow run main.nf --input_files input_files --output output_folder
Input:
* input_files: the path to a tab-separated values file containing in each row the sample name, FASTQ 1 and FASTQ 2
The input file does not have header!
Example input file:
name1 fastq1.fq.gz fastq2.fq.gz
name2 fastq1.fq.gz fastq2.fq.gz
* output: output folder where results will be stored
Optional input:
* read_length: the read length (default: 50)
* hlahd_folder: the HLA-HD folder (default: /code/hlahd.1.2.0.1)
* bowtie2_folder: the bowtie2 folder (default: /code/bowtie/2.3.4.3)
* bowtie2_module: the module to load with bowtie2
* ld_library_path: the value to set in LD_LIBRARY_PATH
* cpus: the number of CPUs per sample (default: 15)
* memory: the amount of memory per sample (default: 30g)
References
- Kawaguchi S, Higasa K, Shimizu M, Yamada R, Matsuda F. HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data. Hum Mutat. 2017 Jul;38(7):788-797. doi: 10.1002/humu.23230 Add to Citavi project by DOI. Epub 2017 May 12. PMID: 28419628
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. 10.1038/nbt.3820