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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-platypusindelcalling Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// workflow parameters
// Post Processes
runIndelAnnotation = false
runIndelDeepAnnotation = false
runIndelVCFFilter = false
runTinda = false
skip_multiqc = false
standard_vcf = true
// Annotate Table options
padding = 10 // default value
minoverlapfraction = 0.7 // default value
maxborderdist = 20 // default value
maxmatches = 5 // default value
// Filtering options
min_confidence_score = 8 // default value: 8
crit_gnomad_exomes_maxmaf = 0 // default value: 0.001
crit_gnomad_genomes_maxmaf = 0 // default value: 0.001
crit_exac_maxmaf = 0 // default value: 0.01
crit_evs_maxmaf = 0 // default value: 1.0
crit_1kgenomes_maxmaf = 0 // default value: 0.01
crit_localcontrol_maxmaf = 0 // default value: 0.05
filter_non_clinic = false // default value: false
// screenshot options
max_var_screenshots = 100 // default value
window_size = 100 // default value
// runtinda options
seqtype = 'WGS' // WES/WGS
right_border = 0.45 // default value
bottom_border = 0.01 // default value
maf_threshold = 0.001 // default value
//// Files ///
// References
data_path = null // If database files in the same place
genome = "GRCh38" // use igenome or refgenie genome bundle - GRCh38, GRCh37, hg38 or hg37
// Annovar files
annotation_tool = "vep" // or vep
annovar_path = null // path/to/annovar
outdir_cache = null // No output directory for cache
vep_cache = null // No directory for VEP cache
download_cache = false // DO NOT Download annotation cache
// Basic Annotation files
k_genome = null // 1000k genome indels (integrated calls in vcf.gz format along with index)
dbsnp_indel = null // dbSNP indels ( in vcf.gz format along with index)
exac_file = null // ExAC file (integrated calls in vcf.gz format along with index)
evs_file = null // EVS (integrated calls in vcf.gz format along with index)
local_control_wgs = null // Local Control WGS (integrated calls in vcf.gz format along with index)
local_control_wes = null // Local Control WES(integrated calls in vcf.gz format along with index)
gnomad_genomes = null // gnomAD genome INDELs (integrated calls in vcf.gz format along with index)
gnomad_exomes = null // gnomAD exome INDELs (integrated calls in vcf.gz format along with index)
// INDEL reability files
repeat_masker = null // UCSC Repeat Masker file (integrated calls in bed.gz format along with index)
dac_blacklist = null // UCSC DAC blacklist file (integrated calls in bed.gz format along with index)
duke_excluded = null // UCSC DUKE Excluded file (integrated calls in bed.gz format along with index)
hiseq_depth = null // UCSC HiSEQ Depth file (integrated calls in bed.gz format along with index)
self_chain = null // UCSC Self Chain file (integrated calls in bed.gz format along with index)
mapability_file = null // UCSC Mappability file (integrated calls in bed.gz format along with index)
simple_tandemrepeats = null // UCSC Simple Tandem repeats file (integrated calls in bed.gz format along with index)
// Deep Annotation files
enchancer_file = null // UCSC Enhangers file (integrated calls in bed.gz format along with index)
cpgislands_file = null // UCSC CpG Islands file (integrated calls in bed.gz format along with index)
tfbscons_file = null // UCSC TFBS noncoding side file (integrated calls in bed.gz format along with index)
encode_dnase_file = null // UCSC ENCODE DNAase cluster regions file (integrated calls in bed.gz format along with index)
mirnas_snornas_file = null // miRNA snoRNAs file (integrated calls in bed.gz format along with index)
mirna_sncrnas_file = null // miRNA sncRNAs file (integrated calls in bed.gz format along with index)
mirbase_file = null // mirBASE file (integrated calls in bed.gz format along with index)
cosmic_file = null // COSMIC database file (integrated calls in bed.gz format along with index)
mir_targets_file = null // miRNA targets file (integrated calls in bed.gz format along with index)
cgi_mountains_file = null // UCSC CGI mountains file (integrated calls in bed.gz format along with index)
phastconselem_file = null // UCSC Phast Cons Element regions file (integrated calls in bed.gz format along with index)
encode_tfbs_file = null // UCSC ENCODE TFBS cluster regions file (integrated calls in bed.gz format along with index)
// TiNDA files
genemodel_bed = null // Gencode file (integrated calls in bed.gz format along with index)
local_control_tinda_wgs = null // Local Control WGS (integrated calls in vcf.gz format along with index)
local_control_tinda_wes = null // Local Control WES (integrated calls in vcf.gz format along with index)
gnomad_genomes_tinda = null // gnomAD genome INDELs (integrated calls in vcf.gz format along with index)
gnomad_exomes_tinda = null // gnomAD exome INDELs (integrated calls in vcf.gz format along with index)
// igenome References options
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
save_reference = false // Built references not saved
// refgenie References options
refgenie_ignore = false
refgenie_base = "/omics/groups/OE0608/internal/kubran/"
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = 'results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = "reference,input_paths,cluster-options,clusterOptions,project,data_path,gnomadgenomes,gnomadexomes,dbsnp_snv "
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/platypusindelcalling custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/platypusindelcalling.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/platypusindelcalling profiles: ${params.custom_config_base}/pipeline/platypusindelcalling.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' }
dkfz_cluster_37 { includeConfig 'conf/dkfz_cluster_37.config' }
dkfz_cluster_38 { includeConfig 'conf/dkfz_cluster_38.config' }
test_igenomes_38 { includeConfig 'conf/test_igenomes_38.config' }
test_refgenie_38 { includeConfig 'conf/test_refgenie_38.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Load refgenie build genome_config.yaml file
if (!params.refgenie_ignore) {
includeConfig 'conf/refgenie.config'
} else {
params.genomes = [:]
}
// 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}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
prov {
enabled = true
formats {
bco {
file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
}
}
}
manifest {
name = 'nf-platypusindelcalling'
author = 'Kuebra Narci kuebra.narci@dkfz-heidelberg.de'
homePage = 'https://github.com/ghga-de/nf-platypusindelcalling'
description = 'ODCF Platypus based indel calling pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=23.10.3'
version = '2.0.1'
}
// Nextflow plugins
plugins {
id 'nf-prov@1.2.2' // Provenance reports for pipeline runs
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}
process.scratch=true