config.yaml

#NOTE: you won't typically have to change the following two lines!
metasheet: 'metasheet.csv'
ref: "wes/ref.yaml"

somatic_caller: tnscope

#Path to sentieon binary
sentieon_path: "/michorlab/jacobg/wes/sentieon/sentieon-genomics-202010.01/bin/"

#Tell us what assembly to use (!! MUST be defined in chips/ref.yaml !!)
assembly: hg38

vcf2maf_bufferSize: 1000 #for standard8 #50000 for highmem-64

# neoantigen module - Define whether to run class II results
# This will trigger an additional HLA caller, xHLA to generate class II
# HLA alleles.  Comment the following line to DISABLE it-
neoantigen_run_classII: False

# neoantigen module - Define which callers to use in a space-separated list
# Callers avaliable:
# 'MHCflurry', 'MHCnuggetsI', 'MHCnuggetsII', 'NNalign', 'NetMHC',
# 'NetMHCIIpan', 'NetMHCcons', 'NetMHCpan', 'PickPocket', 'SMM',
# 'SMMPMBEC', 'SMMalign'
neoantigen_callers: "NetMHCpan"

# neoantigen module - Define which epitope lengths to analyze in comma
# 	     	      separated list for class1 and class2 respectively
neoantigen_epitope_lengths_cls1: "8,9,10,11"
neoantigen_epitope_lengths_cls2: "12,13,14,15,16,17,18"

#effective_size: # of base-pairs covered in target regions
effective_size: 30000000

tumor_only: False

# DEFINE the samples- each sample should have a name, e.g. SAMPLE1
# and a path to the input file, e.g. data/sample1.fastq.gz
# VALID INPUTS: fastq, fastq.gz, bam
# NOTE: for PAIRED-END fastq/fastq.gz, give both pairs to the sample:
# SAMPLE_1_PE:
#   - data/sample1_pair1.fastq
#   - data/sample1_pair2.fastq
# WARNING: DO not mix Paired-END and Single-End samples!!!
# ALSO: having the string "rep" or '.' in your sample name will throw an ERROR
# '.' causes Rscripts chop off names; and it's used as replicate splitter
samples:
  Pt_4500:
    - /michorlab/zhao_data/wxs/data/SRR7588441_1.fastq
    - /michorlab/zhao_data/wxs/data/SRR7588441_2.fastq
  Pt_3986_NL_AS:
    - /michorlab/zhao_data/wxs/data/SRR7588440_1.fastq
    - /michorlab/zhao_data/wxs/data/SRR7588440_2.fastq
  Pt_4500_NL_AS:
    - /michorlab/zhao_data/wxs/data/SRR7588439_1.fastq
    - /michorlab/zhao_data/wxs/data/SRR7588439_2.fastq






#The following are optional meta information that will be stored in the report
#wes_run_info:
#  wes_commit: c1d74f0
#  wes_ref_snapshot: wes-human-ref-ver1-7
#  wes_image: wes-ver3-01a