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nextflow.config
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nextflow.config
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/*
* -------------------------------------------------
* qbic-pipelines/cellranger Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
// Global default params, used in configs
params {
// Workflow flags
index_file = false
input = null
input_paths = null
outdir = './results'
publish_dir_mode = 'copy'
// Reference
genome = false
prebuilt_reference = false
reference_name = "custom_reference"
save_reference = false
fasta = false
gtf = false
// Boilerplate options
multiqc_config = false
email = false
email_on_fail = false
max_multiqc_email_size = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = 's3://ngi-igenomes/igenomes'
tracedir = "${params.outdir}/pipeline_info"
igenomes_ignore = true
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_name = null
config_profile_description = false
config_profile_contact = false
config_profile_url = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,input_paths'
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'qbicpipelines/cellranger:1.0'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
profiles {
conda {
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
process.conda = "$projectDir/environment.yml"
}
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
// once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
docker.enabled = false
singularity.enabled = true
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.autoMounts = true
}
podman {
singularity.enabled = false
docker.enabled = false
podman.enabled = true
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
singularity.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = true
charliecloud.enabled = false
}
charliecloud {
singularity.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = true
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_genome { includeConfig 'conf/test_genome.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'qbic-pipelines/cellranger'
author = 'Gisela Gabernet'
homePage = 'https://github.com/qbic-pipelines/cellranger'
description = 'Cell ranger pipeline for single cell RNAseq'
mainScript = 'main.nf'
nextflowVersion = '>=21.04.1'
version = '1.0.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}