#######################
# globe  
#######################
# HiCSnake 流程所在位置
HICSNAKE_HOME: /home/u023/workspace/Pepper2024
# 基因组前缀 ref/$genome.fa
genome: genome
# 酶的识别位点
restriction_sequence: GATC

#######################
# resolutions
#######################    
# 所有分辨率, 最小值为基础分辨率, 其他值应为基础分辨率的整倍
resolutions:
  - 1000
  - 2000
  - 5000
  - 10000
  - 15000
  - 20000
  - 25000
  - 40000
  - 100000
  - 250000
  - 500000
  - 1000000
# CALDER2 的分辨率, 10kb~100kb, 可设置多个 
Compartment_resolution:
  - 40000
# hicFindTADs 的分辨率, 40kb ~ 100kb, 可设置多个
TAD_resolution:
  - 40000
# Mustache 的分辨率, 1kb ~ 20kb, 可设置多个
Loop_resolution:
  - 10000
Plot_matrix_resolution:
  - 40000

#######################
# paramaters  
#######################
# fastp 过滤
fastp: "--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --qualified_quality_phred 20 --length_required 50"
# 构建矩阵 
hicBuildMatrix: "--minDistance 500 --maxLibraryInsertSize 1500 --inputBufferSize 1000000 --restrictionSequence GATC --danglingSequence GATC"
# 样本间标准化, 不用改
hicNormalize: "--normalize smallest"
# 参考https://github.com/TaoYang-dev/hicrep 
hicrep: "--h 20 --dBPMax 500000"
# 计算分辨率
hicres: "--resolutions 1000,2000,5000,10000"
# 使用 Calder2 检测 subcompartment, -f 指定 feature track, --chr_prefix 指定原染色体前缀,需要统一
calder: "-g others -f ref/gene_density.bed --chr_prefix Chr"
# TAD 检测 
hicFindTADs: " --correctForMultipleTesting fdr --thresholdComparisons 0.01 --delta 0.01"
hicDifferentialTAD: "--pValue 0.05 --mode all --modeReject one"
# Loops 检测
mustache: "" # -pt 0.05 -st 0.88
diff_mustache: "" # -pt 0.05 -pt2 0.05 -st 0.88
hicPlotDistVsCounts: ""
