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nextflow.config
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nextflow.config
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/*
* This configuration file is main one. This includes the pipeline parameters
* and different config files, one for each profile.
* You can switch among them using the Nextflow parameter -profile <<PROFILENAME>>
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
geneidx nextflow parameters config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// include the pipeline parameters from this file
includeConfig "$projectDir/params.config"
params {
// Boilerplate options
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '10.GB'
max_cpus = 8
max_time = '240.h'
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
// this should help in removing the "work" directory after the processes have finished successfully if true
cleanup = false
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
geneidx running config file
Modules configuration
Containers and labels
Profiles
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
process {
// indicates the default container to be used if not defined within the modules
// container = 'ferriolcalvet/geneid-fetching:latest'
withLabel: geneidx {
container = "docker.io/emiliorighi/geneidx:v2"
}
withLabel: samtools {
container = "quay.io/biocontainers/samtools:1.15--h1170115_1"
}
withLabel: diamond {
container = "quay.io/biocontainers/diamond:0.9.30--h56fc30b_0"
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 40.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
// custom container options in case you use docker for mapping the users and avoid docker writing files as root
containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
// ***********
// NOT SURE ABOUT THE IMPACT OF THIS CHANGE
// personalize shell execution, done for avoiding errors in grep
// ***********
// shell = ['/bin/bash', '-euo', 'pipefail']
shell = ['/bin/bash','-u']
}
// include the base configuration
includeConfig 'conf/base.config'
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
manifest {
name = 'GeneidX'
author = 'Ferriol Calvet (and masking from nf-core genomeannotator )'
homePage = 'https://github.com/guigolab/geneidx'
description = 'Annotation of eukaryotic genomes'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '0.1'
}
// TODO revise if we want to update the minimal version
// 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
}
}
}