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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/genomeassembler Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = 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 = false
help_full = false
show_hidden = 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
// Pipeline params
input = '' // input file
outdir = null // outdir
use_ref = true // use a reference genome (requires fasta + gff)
skip_alignments = false // Intended for QC-oriented (re)-runs, alignments (to ref) are provided
skip_assembly = false // Intended for QC-oriented (re)-runs, assemblies are provided
// -- ONT
ont = false // ont reads available?
collect = false // collect ONT reads into a single file
porechop = false // run porechop on ONT
read_length = null // avg read length, can be estimated from reads
// -- Jellyfish (ONT reads only) --
jellyfish = true // run jellyfish
dump = false // dump output
kmer_length = 21 // kmer length
// -- HiFi --
hifi = false // HiFi reads available?
lima = false // run lima on HiFi reads?
pacbio_primers = null // if lima, then this needs to be a path to a list of primers
// -- ASSEMBLY
assembler = "flye" // assembler to use
// -- Assembly: Flye --
genome_size = null // genomesize, optional, can be estimated from ONT reads
flye_mode = '--nano-hq' // flye mode
flye_args = "" // extra flye args
// -- Assembly: hifiasm --
hifiasm_ont = false // combine hifi and ONT with hifiasm --ul?
hifiasm_args = "" // extra hifiasm args
// -- Short read --
short_reads = false // short reads available?
trim_short_reads = true // trim short reads?
// -- POLISHING
// -- Polish: medaka
polish_medaka = false // run medaka
medaka_model = "" // model for medaka, if empty medaka will guess
// -- Polish: pilon
polish_pilon = false // run pilon
// -- QC --
// -- QC : Meryl, automatically enabled with short-reads
meryl_k = 21 // k for meryl
merqury = true
// -- QC : Busco
busco = true // run busco
busco_db = '' // path to busco db
busco_lineage = "brassicales_odb10" // busco lineage
// -- QC: QUAST
quast = true // run quast
qc_reads = "ONT" // if both ONT and HiFi reads are available, which should be used for QC alignments
// -- SCAFFOLDING
scaffold_links = false // Scaffold with LINKS
scaffold_longstitch = false // Scaffold with Longstitch
scaffold_ragtag = false // Scaffold with ragtag
// -- ANNOTATIONS
lift_annotations = true // lift annotations from reference (if reference is provided)
}
// 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
dumpHashes = 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'
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
hifi_flye { includeConfig 'configs/hifi_flye.config' } // Hifi-reads with flye
hifi_hifiasm { includeConfig 'configs/hifi_hifiasm.config' } // hifi-reads with hifiasm
ont_flye { includeConfig 'configs/ont_flye.config' } // ont-reads with flye
ont_hifiasm { includeConfig 'configs/ont_hifiasm.config' } // ont-reads with hifiasm
hifiont_hifiasm { includeConfig 'configs/hifi_ont_hifiasm_ul.config' } // ont and hifi reads with hifiasm --ul
hifiont_flyehifiasm { includeConfig 'configs/hifi_ont_flye_on_hifiasm.config' } // ont and hifi reads. ONT via flye, Hifi via hifiasm, scaffold flye on hifiasm
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/genomeassembler custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/genomeassembler.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",
"-C", // No clobber - prevent output redirection from overwriting files.
"-e", // Exit if a tool returns a non-zero status/exit code
"-u", // Treat unset variables and parameters as an error
"-o", // Returns the status of the last command to exit..
"pipefail" // ..with a non-zero status or zero if all successfully execute
]
// 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 = 'nf-core/genomeassembler'
author = """Niklas Schandry"""
contributors = [
[
name: 'Niklas Schandry',
affiliation: 'LMU Munich, Faculty of Biology, Genetics',
email: '[email protected]',
github: '@nschan',
contribution: ['author', 'maintainer'],
orcid: '0000-0003-3099-7860'
]
]
homePage = 'https://github.com/nf-core/genomeassembler'
description = """Assemble genomes from long ONT or pacbio HiFi reads"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '1.0.1dev'
doi = '10.5281/zenodo.14986998'
}
// 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[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${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/modules.config'