spechla

Profile HLA alleles from paired-end read DNA or RNA FASTQ files using SpecHLA

usage

nexus run --nf-workflow hla_typing_spechla.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_spechla "-u 0"

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_spechla	spechla extra CLI parameters (default: ‘“-u 0”’). Use -u 0 for full-length or -u 1 for exome or RNA data. Note that the parameters need to be wrapped in quotes.