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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 using --input_fastqs.

Sample name	FASTQ1	FASTQ2
sample_1	/path/to/sample_1.1.fq.gz	/path/to/sample_1.2.fq.gz
sample_2	/path/to/sample_2.1.fq.gz	/path/to/sample_2.2.fq.gz

Alternatively, provide a table with BAM files using --input_bams.

Sample name	BAM
sample_1	/path/to/sample_1.bam
sample_2	/path/to/sample_2.bam

BAM files should be indexed.

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_fastqs: 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
    * input_bams: the path to a tab-separated values file containing in each row the sample name and BAM
    The input file does not have header!
    Example input file:
    name1       name1.bam
    name2       name2.bam
    * output: output folder where results will be stored

Optional input:
    * reference: the reference genome to use (default: hg38, possible values: hg38 or hg19)
    * 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