https://github.com/connor-lab/ncov2019-artic-nf
Tip revision: 8af5152cf7107c3a369b996f5bad3473d329050c authored by Matt Bull on 08 April 2021, 15:56:30 UTC
Fix params.gff undefined and remove CLIMB upload (#99)
Fix params.gff undefined and remove CLIMB upload (#99)
Tip revision: 8af5152
nextflow.config
// Global default params, used in configs
params {
// Workflow flags
outdir = './results'
// Boilerplate options
help = false
tracedir = "${params.outdir}/pipeline_info"
// cache option makes it a bit easier to set conda or singularity cacheDir
cache = ''
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
if ( params.medaka || params.nanopolish ){
includeConfig 'conf/nanopore.config'
}
if ( params.illumina ){
includeConfig 'conf/illumina.config'
}
profiles {
conda {
if ( params.medaka || params.nanopolish ) {
process.conda = "$baseDir/environments/nanopore/environment.yml"
} else if (params.illumina) {
process.conda = "$baseDir/environments/illumina/environment.yml"
}
if (params.cache){
conda.cacheDir = params.cache
}
includeConfig 'conf/conda.config'
}
docker {
docker.enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
if ( params.medaka || params.nanopolish ){
process.container = "file:///${baseDir}/artic-ncov2019-nanopore.sif"
} else if (params.illumina) {
process.container = "file:///${baseDir}/artic-ncov2019-illumina.sif"
}
if (params.cache){
singularity.cacheDir = params.cache
}
}
slurm {
process.executor = 'slurm'
}
lsf {
process.executor = 'lsf'
}
gls {
process.executor = 'google-lifesciences'
includeConfig 'conf/gls.config'
}
}
// COG-UK institutional config
includeConfig 'conf/coguk.config'
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = false
file = "${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'
}