Revision e061d26891b972d699a8263db7d53198572af237 authored by Matt Bull on 02 April 2020, 08:52:13 UTC, committed by Matt Bull on 02 April 2020, 08:52:13 UTC
1 parent 60623fb
nextflow.config
// Global default params, used in configs
params {
// Workflow flags
outdir = './results'
// Boilerplate options
help = false
tracedir = "${params.outdir}/pipeline_info"
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
includeConfig 'conf/resources.config'
if ( params.medaka || params.nanopolish ){
includeConfig 'conf/nanopore.config'
}
if ( params.illumina ){
includeConfig 'conf/illumina.config'
}
profiles {
conda {
if (params.medaka){
process.conda = "$baseDir/environment-medaka.yml"
} else if (params.nanopolish) {
process.conda = "$baseDir/environment.yml"
} else if (params.illumina) {
process.conda = "$baseDir/environment-illumina.yml"
}
}
docker {
docker.enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
if (params.medaka){
process.container = "file:///${baseDir}/artic-ncov2019-medaka.sif"
} else if (params.nanopolish) {
process.container = "file:///${baseDir}/artic-ncov2019-nanopolish.sif"
} else if (params.illumina) {
process.container = "file:///${baseDir}/artic-ncov2019-illumina.sif"
}
}
slurm {
process.executor = 'slurm'
includeConfig 'conf/slurm.config'
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = false
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = false
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = false
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = false
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
author = 'Matt Bull'
description = 'Nextflow for running the Artic ncov2019 pipeline'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = '0.1.0'
}
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