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nextflow.config
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nextflow.config
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/*
========================================================================================
QUANTS Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
input_type = "fastq"
single_end = false
// Read transformation
read_transform = null
// Read merging
read_merging = null
read_merging_qc = false
seqprep_options = null
flash2_options = null
// Adapter trimming and QC
adapter_trimming = null
adapter_trimming_qc = false
adapter_cutadapt_options = null
// Primer trimming and QC
primer_trimming = null
primer_trimming_qc = false
primer_cutadapt_options = null
// Read length filtering
read_filtering = null
read_filtering_qc = false
seqkit_seq_options = null
// Modify FASTQ (e.g. add perfect primer sequence to reads)
read_modification = false
append_start = null
append_end = null
append_quality = null
// Quantification
quantification = null
oligo_library = null
transform_library = false
pyquest_library_converter_options = null
// Sequencing QC
raw_sequencing_qc = false
seqkit_stats_options = null
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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 {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'cancerit/QUANTS'
author = 'Victoria Offord'
homePage = 'https://gitlab.internal.sanger.ac.uk/team113_nextflow_pipelines/QUANTS'
description = 'Analysis pipeline for saturation genome editing screens'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.6'
version = '3.0.0.3'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}