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params {
fastq = 'fastq/*_{1,2}.*'
genomeSize = 0.01
minCoverage = 10
adapters = 'None'
trimSlidingWindow = '5:20'
trimLeading = 3
trimTrailing = 3
trimMinLength = 55
clearInput = false
pattern = 'A 50%; T 50%; N 50%'
reference = 'ref/DENV_MAPPING_V3.fasta'
index = null
minimumContigSize = 10000
spadesMinCoverage = 2
spadesMinKmerCoverage = 2
spadesKmers = 'auto'
megahitKmers = 'auto'
minAssemblyCoverage = 'auto'
AMaxContigs = 1000
splitSize = 10000
typingReference = 'ref/DENV_TYPING_V3.fasta'
includeNCBI = true
getGenome = true
substitutionModel = 'GTRGAMMA'
seedNumber = 12345
bootstrap = 500
simpleLabel = true
}
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