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nextflow.config
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nextflow.config
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manifest {
author = 'Dan Fornika <dan.fornika@bccdc.ca>'
description = 'Generate Simulated Reads from Ref Genomes'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = '0.1.0'
}
params {
flat = false
keep_bams = false
assembly_exts = ['*.fa', '*.fasta', '*.fna']
assembly_search_path = makeAssemblySearchPath( assembly_exts )
contaminants = 'NO_FILE'
depths_file = 'NO_FILE'
depth = 30
read_length = 150
mean_fragment_length = 400
stdev_fragment_length = 100
quality_shift_r1 = 0
quality_shift_r2 = 0
replicates = 1
collect_outputs = false
collected_outputs_prefix = 'collected'
}
def makeAssemblySearchPath ( assembly_exts ) {
def assembly_search_path = []
for (ext in assembly_exts) {
assembly_search_path.add(params.assembly_input.toString() + '/' + ext.toString())
assembly_search_path.add(params.assembly_input.toString() + '/*/' + ext.toString())
}
return assembly_search_path
}
profiles {
conda {
process.conda = "$baseDir/environments/environment.yml"
if (params.cache){
conda.cacheDir = params.cache
}
}
}
process {
withName: bwa_align {
cpus = 4
}
}