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nextflow.config
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nextflow.config
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// config defaults
params {
// workflow options
outdir = "3_nextflow_pipeline_results"
publish_dir_mode = 'copy'
// which steps to run?
trim = true
align = true
// STAR options
sparse_d = 1
index_bases = 13
// MULTIQC options
multiqc_config = "$baseDir/assets/multiqc_config.yml"
// default job options
max_memory = '96.GB'
max_cpus = 8
max_time = '72.h'
// disable conda by default
enable_conda = false
// config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
}
// 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: ${params.custom_config_base}/nfcore_custom.config")
}
// profiles for various environments
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.userEmulation = true
params.enable_conda = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
params.enable_conda = false
}
// variables for testing
test {includeConfig 'conf/test.config'}
// config for running on the imperial cluster
imperial_rcs {includeConfig 'conf/imperial_rcs.config'}
}
manifest {
name = 'jackgisby/ReCoDE_rnaseq_pipeline'
author = 'Jack Gisby'
homePage = 'https://github.com/ImperialCollegeLondon/ReCoDE_rnaseq_pipeline'
description = 'A parallelised pipeline for the analysis of RNA sequencing data.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '0.1'
}
// Function to ensure that resource requirements don't go beyond a maximum limit (from nf-core)
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}