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nextflow.config
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nextflow.config
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/*
* -------------------------------------------------
* nf-core/nanoclust Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
// Global default params, used in configs
params {
// Boilerplate options
outdir = './results'
demultiplex = false
demultiplex_porechop = false
multiqc = false
kit = "RAB204"
// UMAP Clustering and polishing parameters
umap_set_size = 100000
cluster_sel_epsilon = 0.5
min_cluster_size = 200
polishing_reads = 100
min_read_length = 1400
max_read_length = 1700
// Classification parameters
db = false
tax = false
name = false
multiqc_config = "$baseDir/assets/multiqc_config.yaml"
email = false
email_on_fail = false
maxMultiqcEmailFileSize = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
tracedir = "${params.outdir}/pipeline_info"
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
}
process {
cpus = 4
withName: demultiplex { cpus = 4 }
withName: QC { cpus = 4 }
withName: kmer_freqs { cpus = 4 }
withName: read_clustering { cpus = 4}
withName: split_by_cluster { cpus = 4}
withName: read_correction { cpus = 4 }
withName: draft_selection { cpus = 4 }
withName: racon_pass { cpus = 4 }
withName: medaka_pass { cpus = 4 }
withName: consensus_classification { cpus = 4 }
withName: output_documentation { cpus = 4 }
withName: fastqc { cpus = 4 }
withName: multiqc { cpus = 4 }
}
profiles {
test { includeConfig 'conf/test.config' }
conda {
process {
withName: demultiplex { conda = "$baseDir/conda_envs/demultiplex/environment.yml" }
withName: demultiplex_porechop { conda = "$baseDir/conda_envs/demultiplex_porechop/environment.yml" }
withName: QC { conda = "$baseDir/conda_envs/qc_fastp/environment.yml" }
withName: fastqc { conda = "$baseDir/conda_envs/fastqc/environment.yml" }
withName: multiqc { conda = "$baseDir/conda_envs/fastqc/environment.yml" }
withName: kmer_freqs { conda = "$baseDir/conda_envs/kmer_freqs/environment.yml" }
withName: read_clustering { conda = "$baseDir/conda_envs/read_clustering/environment.yml" }
withName: split_by_cluster { conda = "$baseDir/conda_envs/split_by_cluster/environment.yml" }
withName: read_correction { conda = "$baseDir/conda_envs/read_correction/environment.yml" }
withName: draft_selection { conda = "$baseDir/conda_envs/draft_selection/environment.yml" }
withName: racon_pass { conda = "$baseDir/conda_envs/racon_pass/environment.yml" }
withName: medaka_pass { conda = "$baseDir/conda_envs/medaka_pass/environment.yml" }
withName: consensus_classification { conda = "$baseDir/conda_envs/consensus_classification/environment.yml" }
withName: get_abundances { conda = "$baseDir/conda_envs/cluster_plot_pool/environment.yml" }
withName: plot_abundances { conda = "$baseDir/conda_envs/cluster_plot_pool/environment.yml" }
withName: output_documentation { conda = "$baseDir/conda_envs/output_documentation/environment.yml" }
}
}
docker {
docker.enabled = true
//process.container = 'nf-core/nanoclust:latest'
process {
withName: demultiplex { container = 'hecrp/nanoclust-demultiplex' }
withName: demultiplex_porechop { container = 'hecrp/nanoclust-demultiplex_porechop' }
withName: QC { container = 'hecrp/nanoclust-qc' }
withName: fastqc { container = 'hecrp/nanoclust-fastqc' }
withName: multiqc { container = 'hecrp/nanoclust-fastqc' }
withName: kmer_freqs { container = 'hecrp/nanoclust-kmer_freqs' }
withName: read_clustering { container = 'hecrp/nanoclust-read_clustering' }
withName: split_by_cluster { container = 'hecrp/nanoclust-split_by_cluster' }
withName: read_correction { container = 'hecrp/nanoclust-read_correction' }
withName: draft_selection { container = 'hecrp/nanoclust-draft_selection' }
withName: racon_pass { container = 'hecrp/nanoclust-racon_pass' }
withName: medaka_pass { container = 'hecrp/nanoclust-medaka_pass' }
withName: consensus_classification { container = 'hecrp/nanoclust-consensus_classification'
docker.temp = "$baseDir/" }
withName: get_abundances { container = 'hecrp/nanoclust-plot_abundances' }
withName: plot_abundances { container = 'hecrp/nanoclust-plot_abundances' }
withName: output_documentation { container = 'hecrp/nanoclust-output_documentation' }
}
}
}
// 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Avoid this error:
// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, once this is established and works well, nextflow might implement this behavior as new default.
docker.runOptions = '-u \$(id -u):\$(id -g)'
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
name = 'genomicsITER/nanoclust'
author = 'Hector Rodriguez-Perez, Laura Ciuffreda'
homePage = 'https://github.com/nf-core/nanoclust'
description = 'De novo clustering and consensus building for ONT 16S sequencing data'
mainScript = 'main.nf'
nextflowVersion = '>=0.32.0'
version = '1.0dev'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}