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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genomic-medicine-sweden/nallo Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
target_regions = null
cadd_resources = null
cadd_prescored_indels = null
filter_variants_hgnc_ids = null
par_regions = null
tandem_repeats = null
trgt_repeats = null
stranger_repeat_catalog = null
genmod_reduced_penetrance = null
genmod_score_config_snvs = null
genmod_score_config_svs = null
echtvar_snv_databases = null
svdb_sv_databases = null
variant_consequences_snvs = null
variant_consequences_svs = null
vep_cache = null
vep_plugin_files = null
hificnv_expected_xy_cn = null
hificnv_expected_xx_cn = null
hificnv_excluded_regions = null
somalier_sites = null
// Skip parts of the workflow
skip_genome_assembly = params.preset == 'ONT_R10' ? true : false
skip_call_paralogs = false
skip_cnv_calling = false
skip_alignment = false
skip_methylation_pileups = params.preset == 'pacbio' ? true : false
skip_phasing = false
skip_qc = false
skip_rank_variants = false
skip_repeat_calling = params.preset == 'ONT_R10' ? true : false
skip_repeat_annotation = params.preset == 'ONT_R10' ? true : false
skip_snv_calling = false
skip_snv_annotation = false
skip_sv_annotation = false
deepvariant_model_type = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO'
minimap2_read_mapping_preset = params.preset == 'ONT_R10' ? 'lr:hq' : 'map-hifi'
filter_snvs_expression = ''
filter_svs_expression = ''
phaser = 'longphase'
sv_caller = 'severus'
preset = 'revio'
hifiasm_mode = 'hifi-only'
snv_caller = 'deepvariant'
vep_cache_version = 110
// Test config options
extra_modkit_options = ''
extra_vep_options = ''
extra_paraphase_options = ''
extra_hifiasm_options = ''
// Preprocessing/parallelisation
snv_calling_processes = 13
alignment_processes = 8
// References
fasta = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/ba720cd29322036d966ab3e4bc4c3d03e1731af5/'
// 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'
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
conda.channels = ['conda-forge', 'bioconda']
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' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'genomic-medicine-sweden/nallo'
author = """Felix Lenner"""
homePage = 'https://github.com/genomic-medicine-sweden/nallo'
description = """Long-read variant calling pipeline"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '0.4.0'
doi = '10.5281/zenodo.13748210'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
\033[0;34m _ _ _ _
\033[0;34m __ _ ___ _ __ ___ _ __ ___ (_) ___ _ __ ___ ___ __| (_) ___(_)_ __ ___
\033[0;34m / _` |/ _ \\ '_ \\ / _ \\| '_ ` _ \\| |/ __|____| '_ ` _ \\ / _ \\/ _` | |/ __| | '_ \\ / _ \\_____
\033[0;34m | (_| | __/ | | | (_) | | | | | | | (_|_____| | | | | | __/ (_| | | (__| | | | | __/_____|
\033[0;34m \\__, |\\___|_| |_|\\___/|_| |_| |_|_|\\___| |_| |_| |_|\\___|\\__,_|_|\\___|_|_| |_|\\___|
\033[0;34m |___/ _____ __| | ___ _ __ / / __ __ _| | | ___
\033[0;34m / __\\ \\ /\\ / / _ \\/ _` |/ _ \\ '_ \\ / / '_ \\ / _` | | |/ _ \\
\033[0;34m \\__ \\\\ V V / __/ (_| | __/ | | |/ /| | | | (_| | | | (_) |
\033[0;34m |___/ \\_/\\_/ \\___|\\__,_|\\___|_| |_/_/ |_| |_|\\__,_|_|_|\\___/
\033[0;34m
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies\n https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/base.config'
includeConfig 'conf/modules/annotate_cadd.config'
includeConfig 'conf/modules/annotate_consequence_pli.config'
includeConfig 'conf/modules/annotate_repeat_expansions.config'
includeConfig 'conf/modules/annotate_svs.config'
includeConfig 'conf/modules/general.config'
includeConfig 'conf/modules/bam_infer_sex.config'
includeConfig 'conf/modules/call_cnvs.config'
includeConfig 'conf/modules/call_paralogs.config'
includeConfig 'conf/modules/call_repeat_expansions.config'
includeConfig 'conf/modules/call_svs.config'
includeConfig 'conf/modules/convert_input_files.config'
includeConfig 'conf/modules/filter_variants.config'
includeConfig 'conf/modules/assembly_variant_calling.config'
includeConfig 'conf/modules/genome_assembly.config'
includeConfig 'conf/modules/methylation.config'
includeConfig 'conf/modules/phasing.config'
includeConfig 'conf/modules/prepare_genome.config'
includeConfig 'conf/modules/qc_aligned_reads.config'
includeConfig 'conf/modules/scatter_genome.config'
includeConfig 'conf/modules/rank_variants.config'
includeConfig 'conf/modules/short_variant_calling.config'
includeConfig 'conf/modules/snv_annotation.config'
includeConfig 'conf/modules/short_variant_calling.config'