seq2hla

Profile HLA alleles using paired-end RNA sequencing FASTQ files using Seq2HLA

usage

nexus run --nf-workflow hla_typing_seq2hla.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_seq2hla ""

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fastq_file_1’, ‘fastq_file_2’.
--output_dir	Directory to which output files will be copied.
--params_seq2hla	Seq2HLA parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.