nf_dada2_sample_config_V4.txt

// I-O params
params.batchid  = "dada2-run-with-V4-experiment1"
params.ticket   = '8259'
params.inputdir = "/home/projects/May2018-metagenomcis/data/reads/V4_Experiment1"
params.reads    = "${params.inputdir}/*_R{1,2}.fastq"
params.outdir   = "/home/projects/May2018-metagenomcis/results/20180525_dada2-run-with-V4-experiment1"
params.email    = 'userid@illinois.edu'
params.metaconfig = "/home/projects/May2018-metagenomcis/src/dada2.sample.mapping.file.V4experiment1.txt"


// Trimming
params.trimFor = 19 
params.trimRev = 20
params.truncFor = 0 
params.truncRev = 0
params.maxEEFor = 2
params.maxEERev = 2
params.truncQ = 2
params.maxN = 0
params.maxLen = "Inf"
params.minLen = 20
params.rmPhiX = "FALSE"

// Merging
params.minOverlap = 20
params.maxMismatch = 1
params.trimOverhang = "TRUE" // This should be true with some sequences (V4)

// taxonomy databases, one with genus-level info and one with species-level information
params.reference = "/home/projects/May2018-metagenomcis/data/silva/dada2/silva_nr_v132_train_set.fa"
params.species   = "/home/projects/May2018-metagenomcis/data/silva_species_assignment_v132.fa"

// This proces is optional
params.skipMakeTree = "FALSE"

// NYI, for dada sample inference pooling (requires all samples)
params.pool = false

// trace file
trace {
    enabled = true
    file = "${params.batchid}" + "_pipeline_trace.txt"
    fields = 'task_id,hash,name,status,exit,module,queue,cpus,time,memory,submit,start,complete,realtime,%cpu,rss,rchar,wchar'
}