# pipeline parameters
fullpipeline: true
maponly: false
cageronly: false
gtf: "reproduce_test_data/sacCer3chrIII.gtf"

# preprocessing parameters
input: "/mnt/biggley/home/slava/projects/leancage_dev/test_samplesheet/samplesheet.csv"
infolder:
outdir: "results_nfcore_standard_samplesheet"
sample_name_fields: 1
genome_name: "sacCer3chrIII"
genome:
fasta: "reproduce_test_data/sacCer3chrIII.fa"
index:
seq_platform: "illumina"
seq_center: false
# whether to take the uniquely mapped only
unique_only: true
# whether to remove reads that do not start with G
remove_non_g: false
# whether to trim G or not
nogtrim: false
# mapper to use
bowtie2: false
# dedup
dedup: false

# CAGEr parameters
cager_sample_file: ../cageseq2_sample_list_test.csv
# datatype: "bam" or "bigwig". if bowtie2 is used, it will be set to bam
datatype: "bigwig"
# BSgenome
forgeseed:
sourcedir:
bsgenome: "reproduce_test_data/BSgenome.sacCer3ChrIII.Test.sacCer3ChrIII_1.0.tar.gz"
# parameter for correlation calculation
corrplot_tagCountThreshold: 1
# parameters for normalization
norm_range_min: 5
norm_range_max: 10000
norm_method: "powerLaw"
alpha:
t_norm: 1000000
# parameters for tag clustering
sample_num_thr: 2 # 1
ctss_thr: 3 # 1
distclu_maxDist: 20
keepSingletonsAbove: 1
iq_low: 0.1
iq_high: 0.9
# plotting for tagclusters QC
iqw_tpm_threshold: 3
tssregion_up: -3000
tssregion_down: 3000
tsslogo_upstream: 35
# parameters for consensus clusters
consensus_thr: 2
consensus_dist: 20
# parameters for enhancer calling
cfBalanceThreshold: 0.65 # 0.95
unexpressed: 0
minSamples: 0