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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/pgdb Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// process flag variables
input = 'dump_input.csv'
enable_conda = false
ncrna = false
pseudogenes = false
altorfs = false
vcf = false
cbioportal = false
cosmic = false
cosmic_celllines = null
cosmic_dababase_version = 'latest'
ensembl = false
gnomad = false
add_reference = true
//local COSMIC files
cosmicgenes = null
cosmicmutations = null
cosmiccelllines_genes = null
cosmiccelllines_mutations = null
// Output results
outdir = './results'
// Clean database options
clean_database = false
minimum_aa = 6
add_stop_codons = true
// data download variables
cosmic_user_name = null
cosmic_password = null
// config files
ensembl_downloader_config = "$projectDir/conf/ensembl_downloader_config.yaml"
ensembl_config = "$projectDir/conf/ensembl_config.yaml"
cosmic_config = "$projectDir/conf/cosmic_config.yaml"
cbioportal_config = "$projectDir/conf/cbioportal_config.yaml"
protein_decoy_config = "$projectDir/conf/protein_decoy.yaml"
// ENSEMBL parameters
ensembl_name = 'homo_sapiens'
/* Biotype groups according to:
* https://www.ensembl.org/Help/Faq?id=468 and
* http://vega.archive.ensembl.org/info/about/gene_and_transcript_types.html
*/
biotypes = [
'protein_coding': "protein_coding,polymorphic_pseudogene,non_stop_decay,nonsense_mediated_decay,IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,TR_C_gene,TR_D_gene,TR_J_gene,TR_V_gene,TEC",
'pseudogene': "pseudogene,IG_C_pseudogene,IG_J_pseudogene,IG_V_pseudogene,IG_pseudogene,TR_V_pseudogene,TR_J_pseudogene,processed_pseudogene,rRNA_pseudogene,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,unitary_pseudogene,unprocessed_pseudogene,translated_processed_pseudogene",
'ncRNA': "lncRNA,Mt_rRNA,Mt_tRNA,miRNA,misc_RNA,rRNA,retained_intron,ribozyme,sRNA,scRNA,scaRNA,snRNA,snoRNA,vaultRNA",
]
// vcf-to-proteindb parameters
vcf = false
vcf_file = null
cosmic_cancer_type = 'all'
cosmic_cellline_name = 'all'
cbioportal_study_id = 'all'
cbioportal_accepted_values = 'all'
cbioportal_filter_column = 'CANCER_TYPE'
af_field = null // set to empty when AF_field does not exist in the INFO filed or filtering on AF is not desired
// Output parameters
final_database_protein = "final_proteinDB.fa"
// Decoy options
decoy_prefix = "Decoy_"
decoy = false
decoy_method = "decoypyrat"
decoy_enzyme = "Trypsin"
// gencode download parameters
gencode_url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19"
gnomad_file_url = "gs://gnomad-public/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.*.vcf.bgz"
gnomad_file_url = "gs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz" // use for testing the pipeline, smaller file - only exomes
publish_dir_mode = 'copy'
// Boilerplate options
email = null
email_on_fail = null
max_multiqc_email_size = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
tracedir = "${params.outdir}/pipeline_info"
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = null
config_profile_name = null
config_profile_description = null
config_profile_contact = null
config_profile_url = null
validate_params = true
show_hidden_params = false
schema_ignore_params = 'biotypes'
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/pgdb custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/pgdb.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/pgdb profiles: ${params.custom_config_base}/pipeline/pgdb.config")
// }
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_cosmic_cbio { includeConfig 'conf/test_cosmic_cbio.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/pgdb'
author = 'Husen M. Umer & Yasset Perez-Riverol'
homePage = 'https://github.com/nf-core/pgdb'
description = 'Proteogenomics database creation workflow using pypgatk framework. '
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.1dev'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}