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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ebi-metagenomics/miassembler Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
plugins {
id 'nf-schema'
}
// Global default params, used in configs
params {
// Input options
study_accession = null
reads_accession = null
private_study = false
// For already fetched data
samplesheet = null
/*
* Assembler options, by default the pipeline will pick
* - metaspades for pair-end
* - megahit for single-end
*
* Setting --assembler will force the assembler
*
* - spades: Use for assembling single end reads
*
* - metaspades: Use for assembling paired end reads
* with moderate memory and runtime requirements
*
* - megahit: Use when memory or runtime requirements
* for metaspades are prohibitively high, such as:
* - Memory >1TB
* - Runtime >3-4 days
*/
assembler = null
// The pipeline will use the metadata from ENA (obtained by the fetch_tool)
// As the metadata can be incorrect, we provide the following parameters to
// "force" them
single_end = null
library_layout = null
library_strategy = null
// Reads QC filtering options
filter_ratio_threshold = 0.9
low_reads_count_threshold = 1000
// Reference genome
reference_genome = null
remove_human_phix = true
human_phix_blast_index_name = "human_phix"
human_phix_bwamem2_index_name = "human_phix"
bwamem2_reference_genomes_folder = ""
blast_reference_genomes_folder = ""
// Assembly options
spades_only_assembler = true
min_contig_length = 500
min_contig_length_metatranscriptomics = 200
assembly_memory = 100
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = "results"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '1.TB'
max_cpus = 32
max_time = '168.h' // 7 days
// Assembler versions
spades_version = "3.15.5"
megahit_version = "1.2.9"
}
validation {
failUnrecognisedParams = true
lenientMode = false
showHiddenParams = false
}
// 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
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
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
codon_slurm { includeConfig 'conf/codon_slurm.config' }
}
// Test profiles
includeConfig 'conf/test.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]'
}
// 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
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 = 'ebi-metagenomics/miassembler'
author = """Microbiome Informatics Team - EMBL-EBI"""
homePage = 'https://github.com/ebi-metagenomics/miassembler'
description = """Microbiome Informatics metagenomes assembly pipeline"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to return study / reads folder SRPXXX/SRPXXXXXX/SRRYYYY/SRRYYYYYY
def study_reads_folder( meta = null ) {
// The reads accession is used as the id for samplesheets
def reads_accession = meta?.id ?: params.reads_accession
return study_folder( meta ) + "/" + [
reads_accession.substring(0, 7),
reads_accession,
].join("/")
}
// Function to return study folder SRPXXX/SRPXXXXXX
def study_folder( meta = null ) {
def study_accession = meta?.study_accession ?: params.study_accession
return [
study_accession.substring(0, 7),
study_accession,
].join("/")
}
// 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
}
}
}