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nextflow.config
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params {
// Sample preparation options
primers = "$baseDir/data/primers/Primers_A_elife-11282-supp2-v2_PCR1_primers_A_primers_RC.fasta"
adapters = "$baseDir/data/adapters/NexteraPE-PE.fa"
// Configurations
initDir = "$baseDir/data/initdirs/InitDirShiver190405_BQ30/"
config = "$baseDir/data/configs/shiver_config_BQ30_notrimming.sh"
references = "$baseDir/data/references/HIV1_COM_2020_547-9592_DNA.fasta"
// Databases
hostGenome = "$baseDir/data/databases/human_genome_bwa/"
hostGenomeBase = "GRCh38_genome"
hostFasta = false
// Parameters for estimating time of infection
coverage_threshold_eti = '100'
// Output options
tracedir = "${params.outdir}/store"
cache = "${params.outdir}/cache"
// General options
help = false
input = false
outdir = false
init = false
setup = false
large = false
}
process {
errorStrategy = 'retry'
maxRetries = 1
}
profiles {
local {
process.executor = 'local'
cpus = 1
memory = '3G'
}
slurm {
process.executor = 'slurm'
process.clusterOptions = { "-A development --qos low"}
process.cpus = 1
process.memory = '1G'
process.time = '5m'
if ( params.large ) {
includeConfig 'configs/executor_options_large.config'
}
else {
includeConfig 'configs/executor_options.config'
}
}
docker {
docker.enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
process.container = "talnor/hiv_time_analysis:0.2.0"
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
process.container = "talnor/hiv_time_analysis:0.2.0"
if (params.cache) {
singularity.cacheDir = params.cache
env.NXF_TEMP="${params.cache}"
env.NXF_SINGULARITY_LOCALCACHEDIR="${params.cache}"
env.NXF_SINGULARITY_CACHEDIR="${params.cache}"
env.NXF_SINGULARITY_TMPDIR="${params.cache}"
env.SINGULARITY_LOCALCACHEDIR="${params.cache}"
env.SINGULARITY_CACHEDIR="${params.cache}"
env.SINGULARITY_TMPDIR="${params.cache}"
env.SINGULARITY_ROOTFS="${params.cache}"
env.TMPDIR="${params.cache}"
env.TEMPDIR="${params.cache}"
}
}
}
// Nextflow output files
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
description = 'Analysis pipeline for estimation of time of infection of HIV samples in the TIME study'
mainScript = 'main.nf'
version = '0.2.2'
}