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nextflow.config
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nextflow.config
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params {
outdir = './results'
// exclude = 'decoy,random,chrUn,alt,chrEBV,chrM'
freebayesoptions = '--pooled-continuous --pooled-discrete --genotype-qualities --report-genotype-likelihood-max --allele-balance-priors-off --min-alternate-fraction 0.03 --min-repeat-entropy 1 --min-alternate-count 2'
sexchroms = 'X,Y'
exclude = "~^HLA,~^hs,~:,~^GL,~M,~EBV,~^NC,~^phix,~decoy,~random\$,~Un,~hap,~_alt\$"
// preserves more variants from being filtered
sensitive = true
// covviz report
// the point at which we determine a sample is an outlier from the group at any given point
zthreshold = 3.5
// when calculating significance, the Z-score has to be above the threshold for consecutive points up to the total distance set by distance threshold
distancethreshold = 150000
// slop is the distance to add to traces when plotting -- without slop, it's not always clear what happens to the points immediately flanking the area of significant deviation
slop = 500000
// show all traces when analyzing this few samples; ignores z-threshold, distance-threshold, and slop
minsamples = 8
}
process {
time = '12h'
memory = 16.GB
container = 'brwnj/preon:v0.0.5'
cpus = 1
cache = 'lenient'
errorStrategy = { task.attempt < 3 ? 'retry' : 'finish' }
withName: map_reads {
time = '24h'
container = "brwnj/bwa-nf:v0.0.0"
cpus = 32
memory = 370.GB
}
withName: mark_duplicates {
time = '24h'
container = 'broadinstitute/gatk:4.1.8.1'
memory = 370.GB
cpus = 32
}
withName: run_freebayes {
container = 'brwnj/freebayes:v0.0.3'
}
withName: annotate_vcf {
container = 'nfcore/sarekvep:dev.GRCh38'
memory = 8.GB
}
withName: "merge_vcfs|merge_annotated_vcfs" {
container = 'brwnj/freebayes:v0.0.3'
cache = 'deep'
}
withName: smoove_call {
time = '24h'
memory = { 8.GB * task.attempt }
}
withName: smoove_merge {
memory = 16.GB
cache = 'deep'
}
withName: smoove_genotype {
memory = { 8.GB * task.attempt }
}
withName: smoove_square {
memory = 64.GB
cpus = 3
cache = 'deep'
}
withName: run_indexcov {
memory = 8.GB
cache = 'deep'
}
withLabel: 'smoove' {
container = 'brentp/smoove:v0.2.5'
}
withLabel: 'covviz' {
container = 'brwnj/covviz:v1.3.0'
}
withLabel: 'upload' {
container = 'brwnj/preon:v0.0.1'
}
}