config.yaml

species: 'Homo_sapiens' # will support Mus_musculus in the future
hetero_nbits: 0.75      # will be part of future work

### Section 1: required input and output: one set-up per sample (dot (.) means NotAvailable)

dna_tumor_fq1: '.'
dna_tumor_fq2: '.'
dna_normal_fq1: '.'
dna_normal_fq2: '.'
rna_tumor_fq1: '.'
rna_tumor_fq2: '.'
tumor_spec_peptide_fasta: '.'

output_directory: '.'
prefix: '.'

### Section 2: parameters having no default values: one set-up per installation and for all samples
# variables that begins with ssh:// requires the NeohunterRemotePassword environment variable to be set and exported

#netmhcpan_cmd: '/mnt/d/code/netMHCpan-4.0/netMHCpan'
netmhcpan_cmd: '/mnt/d/code/neohunter/netMHCpan-4.1/netMHCpan'
#netmhcstabpan_cmd: 'ssh://zxf@166.111.130.101:50022/data8t_4/zxf/software/netMHCstabpan-1.0/netMHCstabpan'
netmhcstabpan_cmd: 'ssh://zxf@101.6.41.78:50022/data8t_4/zxf/software/netMHCstabpan-1.0/netMHCstabpan'

### Section 3: parameters having some default values

tumor_depth: 5
tumor_vaf: 0.1
normal_vaf: 0.05
tumor_normal_var_qual: 63 # # Equivalent to tlod=6.3 in Mutect2

prep_peplens: '8,9,10,11,12' # for preprocessing # the netmhcpan series cannot handle any peptide consisting of less than 8 or more than 12 amino acids
kept_peplens: '8,9,10,11' # that finally remain after prioritization by the learned predictor

binding_affinity_filt_thres: 1e9 # 693.00 # 693=21*11*3
binding_stability_filt_thres: -1 # 0.1300 # 0.0500 # 0.13/3 rounded up
tumor_abundance_filt_thres: -1 # 1.000 # 0.3300  # 1/3 rounded

agretopicity_thres: 1e9 # 0.100
foreignness_thres: -1 # 1.00e-16

alteration_type: 'snv,indel,fsv,fusion,splicing'

netmhc_ncores: 128
netmhc_nthreads: 2
ergo2_nthreads: 12
fifo_dir: '/tmp'

# You can add tumor_spec_peptide_fasta config params if you would like to run with given MHCs and peptides
# for example:
#   #comma_sep_hla_list: 'HLA-A01:01,HLA-A02:01' # deprecated, please use the HLA fasta comment key. 
#   all_vars_peptide_faa: /path/to/your/peptide_fasta
# where the /path/to/your/peptide_fasta file contains
#   >${vTypes[0]}_${vIDs[0]} MT=${pepseq1} WT=${pepseq2} TPM=100 HLA=HLA-A01:01,HLA-A02:01
#   ${pepseq1}
#   >${vTypes[1]}_${vIDs[1]} MT=${pepseq1} WT=${pepseq2} TPM=100 HLA=HLA-A01:01
#   ${pepseq2}
#   >${vTypes[2]}_${vIDs[2]} MT=${pepseq3} TPM=200 HLA=HLA-A02:01
#   ${pepseq3}
# such that
#   each element of $vTypes can be 'SNV' 'INS' 'DEL' 'FUS' or 'SP' and
#   each element of $vIDs consists of at most 11 alpha-numeric characters and
#   the MT and TPM key-value pairs are required and
#   the WT key-value pair is optional and
#   ${pepseq1} ${pepseq2} ${pepseq3} all consist of capital letters from the alphabet of the 20 standard amino acids