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nextflow.config
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nextflow.config
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/*
========================================================================================
BatchBlaster config
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Boilerplate options
outdir = "${launchDir}/results"
tracedir = "${params.outdir}/pipeline_info"
validate_params = true
show_hidden_params = false
help = false
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '100.GB'
max_cpus = 16
max_time = '240.h'
}
// Process-specific parameters
process {
// Error strategy
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 3
maxErrors = '-1'
// Default resources
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
// Per-process resources
withName:blast{
cpus = 10
memory = { check_max( 2000.MB * task.attempt, 'memory' ) }
time = { check_max( 5.h * task.attempt, 'time' ) }
}
withName:blast_merge{
cpus = 1
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}
withName:parse_blast{
cpus = 4
memory = { check_max( 10.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
} // end of process configs
// Config profiles
profiles {
// Test config (built-in data)
test { includeConfig 'conf/test.config' }
// Docker-based profile
docker {
docker.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Container specifications are here
includeConfig 'conf/docker.config'
}
// Singularity-based profile
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Container specifications are here
includeConfig 'conf/singularity.config'
}
// Profile for the UT HPC cluster
hpc_ut {
includeConfig 'conf/hpc_ut.config'
}
// Profile for the HPC
cluster {
process.executor = 'slurm'
process.errorStrategy = 'retry'
process.maxRetries = 3
// process.clusterOptions = '--job-name=nftax'
// Container specifications are here
// includeConfig 'conf/cluster.config'
}
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
manifest {
name = 'BatchBlaster'
author = 'Vladimir Mikryukov'
homePage = 'https://github.com/vmikk/BatchBlaster'
description = 'Nextflow-based BLAST pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.6'
version = '0.1'
}
// 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
}
}
}