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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-snvcalling Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// workflow parameters
outdir = 'results'
// Post Processes
runSNVAnnotation = true
runArtifactFilter = true
generateExtendedQcPlots = true
runSNVDeepAnnotation = true
runSNVVCFFilter = true
skip_multiqc = false
runCompareGermline = true
runplots = true
runpurest = true
runcontigs = "NONE"
report_json = true
standard_vcf = true
// Confidence Annotation options
confidenceoptions = '-t 500'
annotation_tool = "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
// Control Pileup QUAL options
ctrl_min_base_qual = 13
ctrl_min_base_qual_contigs = 1
// Filter PE options
basequal = 13
mapqual = 30
qualityscore = 'phred'
mismatch_threshold = -1
// Filter VCF for Bias Parameters
biasPValThreshold = 0.01
biasRatioMinimum = 0.53
biasRatioThreshold = 0.63
nReads = 20
nMuts = 4
tha_score_threshold = 0.15
median_filter_threshold = 20
rVcf = 0.1
maxNumOppositeReadsSequencingWeakBias = 0
maxNumOppositeReadsSequenceWeakBias = 0
maxNumOppositeReadsSequencingStrongBias = 1
maxNumOppositeReadsSequenceStrongBias = 1
// Filtering options
min_confidence_score = 8 // default value
crit_gnomad_exomes_maxmaf = 0.001 // default value 0.001
crit_gnomad_genomes_maxmaf = 0.001 // default value 0.001
crit_1kgenomes_maxmaf = 0.01 // default value 0.01
crit_localcontrol_maxmaf = 0.05 // default value 0.05
allele_freq = 0
min_cov = 0
// Plot options
plot_type = "Differences" // Differences|Ratios
// Annovar
// only option is hg19 now!
annovar_path = null // path/to/annovar
buildver = 'hg19' // default value
dbtype = 'wgEncodeGencodeCompV19' // default value
segdupcol = '"SEGDUP"' // default value
cytobandcol = '"CYTOBAND"' // default value
geneannocols = '"ANNOVAR_FUNCTION,GENE,EXONIC_CLASSIFICATION,ANNOVAR_TRANSCRIPTS"' // default value
// VEP
vep_cache_version = null
vep_genome = null
vep_cache = null
download_cache = true // DO NOT Download annotation cache
// Files //
data_path = null // If database files in the same place
genome = "GRCh37" // use igenome or refgenie genome bundle - GRCh38, GRCh37, hg38 or hg37
contig_file = null // path/contigs.tsv
// Annotation files
k_genome = null
dbsnp_snv = null
local_control_wgs = null
local_control_wes = null
gnomad_genomes = null
gnomad_exomes = null
// INDEL reability files
repeat_masker = null
dac_blacklist = null
duke_excluded = null
hiseq_depth = null
self_chain = null
mapability_file = null
simple_tandemrepeats = null
// Deep Annotation files
enchancer_file = null
cpgislands_file = null
tfbscons_file = null
encode_dnase_file = null
mirnas_snornas_file = null
mirna_sncrnas_file = null
mirbase_file = null
cosmic_file = null
mir_targets_file = null
cgi_mountains_file = null
phastconselem_file = null
encode_tfbs_file = null
// igenome References
genome = null
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 = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = "ref_type,input_paths,cluster-options,clusterOptions,project,data_path,runCytoband,rerunfiltering"
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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 = '500.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")
}
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_hg37 { includeConfig 'conf/dkfz_cluster_hg37.config' }
dkfz_cluster_hg38 { includeConfig 'conf/dkfz_cluster_hg38.config' }
dkfz_cluster_test { includeConfig 'conf/dkfz_cluster_test.config' }
test_igenomes_38 { includeConfig 'conf/test_igenomes_38.config' }
test_refgenie_38 { includeConfig 'conf/test_refgenie_38.config' }
test_refgenie_37 { includeConfig 'conf/test_refgenie_37.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.tracedir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
prov
{
enabled = true
formats {
bco {
file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
}
}
}
manifest {
name = 'nf-snvcalling'
author = 'Kuebra Narci [email protected]'
homePage = 'https://github.com/kubranarci/nf-snvcalling'
description = 'ODCF SNV Calling pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=23.10.1'
version = '2.0.2'
}
// Nextflow plugins
plugins {
id '[email protected]' // Provenance reports for pipeline runs
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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