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nextflow.config
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/*
* ------------------------------------------------------
* Based on the nf-core/rnaseq Nextflow base config file
* ------------------------------------------------------
*/
// Include parameters from configuration file
includeConfig "$projectDir/conf/params.config"
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
standard {
includeConfig "$projectDir/conf/base.config"
process.executor = 'local'
process.conda = "$projectDir/envs/environment.yml"
conda.createTimeout = '6 h'
docker.runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
local {
includeConfig "$projectDir/conf/base.config"
process.executor = 'local'
}
stub {
includeConfig "$projectDir/conf/stub.config"
process.executor = 'local'
}
eddie {
includeConfig "$projectDir/conf/eddie.config"
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
eddie_conda {
includeConfig "$projectDir/conf/eddie_conda.config"
process.conda = "$projectDir/envs/environment.yml"
conda.createTimeout = '8 h'
conda.useMamba = params.mamba ? true : false
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
conda {
process.conda = "$projectDir/envs/environment.yml"
conda.enabled = true
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.createTimeout = '8 h'
conda.useMamba = params.mamba ? true : false
}
docker {
docker.runOptions = '-u \$(id -u):\$(id -g)'
docker.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
docker.runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
uge {
process.executor = 'sge'
}
sge {
process.executor = 'sge'
}
slurm {
process.executor = 'slurm'
}
custom_profile {
includeConfig "${params.my_config}"
}
test {
includeConfig 'conf/demo.config'
}
demo {
includeConfig 'conf/demo.config'
}
}
// Add reporting configuration
timeline {
enabled = true
overwrite = true
file = "${params.outdir}/reports/execution_timeline.html"
}
report {
enabled = true
overwrite = true
file = "${params.outdir}/reports/execution_report.html"
}
trace {
enabled = true
overwrite = true
file = "${params.outdir}/reports/execution_trace.txt"
}
dag {
enabled = true
overwrite = true
file = "${params.outdir}/reports/pipeline_dag.svg"
}
manifest {
name = 'evotools/nSPECTRa'
author = 'Andrea Talenti'
homePage = 'https://github.com/evotools/nSPECTRa'
description = 'Nextflow mutation spectra analysis workflow.'
mainScript = 'main.nf'
nextflowVersion = '>=21.04.0'
version = '1.1.3'
}