netmhcpan4

Predict antigen presentation using NetMHCpan 4.x

usage

nexus run --nf-workflow antigen_prediction_netmhcpan4.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --netmhcpan4_home_dir /path/to/dir/ \
    --netmhcpan4 "" \
    --params_netmhcpan4 "-BA -s -l 8,9,10,11"

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’, ‘fasta_file’, ‘mhc_alleles’.
--output_dir	Directory to which output files will be copied.
--netmhcpan4_home_dir	NetMHCpan home directory path.
--netmhcpan4	NetMHCpan executable path.
--params_netmhcpan4	netmhcpan parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.