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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NorwegianVeterinaryInstitute/ALPPACA Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Global default params, used in configs
params {
// Input
input = null
// contamination analysis options
//min_fraction = "0.2"
// analysis options
// analysis options
}
// Define profiles
profiles {
conda {
params.enable_conda = true
apptainer.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
apptainer.enabled = false
params.enable_conda = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
apptainer.enabled = false
params.enable_conda = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
apptainer.enabled = false
params.enable_conda = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
apptainer.enabled = false
params.enable_conda = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
apptainer.enabled = false
params.enable_conda = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
singularity.enabled = false
params.enable_conda = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
//test_contamination { includeConfig 'conf/test_contamination.config' }
}
conda { createTimeout = "120 min" }
// Load config for module-specific options
includeConfig 'conf/base.config'
includeConfig 'conf/modules.config'
// Manifest
manifest {
name = 'NorwegianVeterinaryInstitute/ALPPACA'
author = 'Håkon Kaspersen'
homePage = 'https://github.com/NorwegianVeterinaryInstitute/ALPPACA'
description = 'A Tool for Prokaryotic Phylogeny and Clustering Analysis'
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.1'
version = '2.2.1'
}
// Define variables to prevent local R libraries from conflicting with the container
env {
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}