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---
## Pipeline-specific parameters
# samples with .fastq.gz extenssion must be placed in the RawData folder
sampleID: "example"
# kit and cell parameters
flowcell: FLO-MIN106
kit: SQK-DCS109
#threads
threads : 20
#junction bonus
junc_bonus : 19
#gap opening costs
gap_open_cost : 12
#minimum MAPQ
MAPQ : 0
#guppy
guppy: "/project/owlmayer/Applications/14_MinION/Guppy324/bin/guppy_basecaller"
#minimap2
minimap2 : "/project/owlmayer/Applications/minimap2/./minimap2"
# hmmer folder, NOT THE APPLICATION
hmmer : "/project/owlmayer/Applications/hmmer-3.3/bin/"
#maskTypes
maskRrna : "/project/owlmayer/Applications/18_MinIon_cDNA/maskRrna.txt"
#maskTypes
maskRegions : "/project/owlmayer/Applications/18_MinIon_cDNA/maskRegion.txt"
#featureCounts
featureCounts : "/project/owlmayer/Applications/subread-2.0.0-Linux-x86_64/bin/./featureCounts"