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nextflow.config
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nextflow.config
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/*
========================================================================================
nf-core/mhcquant Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Workflow flags
help = false
input = "sample_sheet.tsv"
outdir = './results'
fasta = "data/*.fasta"
// References
genomes = null
// Workflow options
allele_sheet = null
include_proteins_from_vcf = false
predict_class_1 = false
predict_class_2 = false
refine_fdr_on_predicted_subset = false
schema_ignore_params = 'genomes'
skip_decoy_generation = false
subset_affinity_threshold = 500
variant_annotation_style = "SNPEFF"
variant_frameshift_filter = false
variant_indel_filter = false
variant_reference = "GRCH38"
variant_snp_filter = false
// MultiQC options
skip_multiqc = false
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Workflow defaults
activation_method = 'ALL'
description_correct_features = 0
digest_mass_range = "800:2500"
enzyme = 'unspecific cleavage'
fdr_threshold = 0.01
fdr_level = 'peptide_level_fdrs'
fixed_mods = ' '
fragment_bin_offset = 0
fragment_mass_tolerance = 0.02
klammer = false
max_rt_alignment_shift = 300
number_mods = 3
num_hits = 1
peptide_min_length = 8
peptide_max_length = 12
pick_ms_levels = 2
predict_RT = false
prec_charge = '2:3'
precursor_mass_tolerance = 5
quantification_fdr = null
quantification_min_prob = 0
refine_fdr_on_predicted_subset = false
remove_precursor_peak = false
run_centroidisation = false
skip_quantification = false
spectrum_batch_size = 500
subset_max_train = 0
tracedir = "${params.outdir}/pipeline_info"
use_x_ions = false
use_z_ions = false
use_a_ions = false
use_c_ions = false
use_NL_ions = false
variable_mods = 'Oxidation (M)'
vcf_sheet = null
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://github.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/mhcquant custom config
try {
includeConfig "${params.custom_config_base}/pipeline/mhcquant.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/mhcquant profiles: ${params.custom_config_base}/pipeline/mhcquant.config")
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'nf-core/mhcquant'
author = 'Leon Bichmann, Marissa Dubbelaar'
homePage = 'https://github.com/nf-core/mhcquant'
description = 'Identify and quantify peptides from mass spectrometry raw data'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '2.2.0'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}