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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-cmgg/germline Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
ped = null
watchdir = null
// Pipeline specific parameters
scatter_count = 40
filter = false
annotate = false
gemini = false
add_ped = false
validate = false
roi = null
project = null
skip_date_project = false
only_call = false
only_merge = false
output_genomicsdb = false
callers = "haplotypecaller"
vardict_min_af = 0.1 // Minimum allele frequency for VarDict
normalize = false
output_suffix = ""
only_pass = false
keep_alt_contigs = false
updio = false
automap = false
hc_phasing = false
// Module specific parameters
dragstr = false
somalier_sites = "https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz"
mosdepth_slow = false
merge_distance = 100000
updio_common_cnvs = null
// VEP plugins to use
vep_dbnsfp = false
vep_spliceai = false
vep_spliceregion = false
vep_mastermind = false
vep_maxentscan = false
vep_eog = false
vep_alphamissense = false
// VEP parameters
vep_chunk_size = 50000
vep_merged = true
species = "homo_sapiens"
vep_version = 105.0
vep_cache_version = 105
// VCFanno parameters
vcfanno = false
vcfanno_lua = null
// Automap parameters
automap_repeats = null
automap_panel = null
automap_panel_name = "cmgg_bio"
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = "${projectDir}/assets/CMGG_logo.png"
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// References
cmgg_config_base = "/conf/"
igenomes_base = null //'s3://ngi-igenomes/igenomes'
igenomes_ignore = true
genome = "GRCh38"
genomes_base = "/references/"
genomes_ignore = false
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config"
// Include test data config
includeConfig !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config"
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
nf_test { includeConfig 'conf/nf_test.config' }
seqplorer { includeConfig 'conf/seqplorer.config' }
seqcap { includeConfig 'conf/seqcap.config' }
hypercap { includeConfig 'conf/hypercap.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
failUnrecognisedParams = false
lenientMode = false
defaultIgnoreParams = ['genomes','igenomes_base','test_data']
showHiddenParams = false
help {
enabled = true
//beforeText = TODO
//afterText = TODO
command = "nextflow run nf-cmgg/germline -profile docker --input <samplesheet> --outdir <output_directory>"
}
}
includeConfig !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.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']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html"
}
report {
enabled = true
file = timeline.file.replace("timeline", "report")
}
trace {
enabled = true
file = timeline.file.replace("timeline", "trace")
}
dag {
enabled = true
file = timeline.file.replace("execution_timeline", "pipeline_dag")
}
manifest {
name = 'nf-cmgg/germline'
author = """nvnieuwk"""
homePage = 'https://github.com/nf-cmgg/germline'
description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.0'
version = '1.8.2'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'