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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViroProfiler Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null
outdir = "output"
mode = "all" // ["setup", "all"]
input_contigs = false // false or path to contigs file
reads_type = "raw" // ["raw", "clean"]
// ============================= Database ====================================
db = "${HOME}/viroprofiler"
// ============================= ViroProfiler modules ====================================
use_abricate = false
use_decontam = false
use_eggnog = false
use_dram = true
use_iphop = true
use_kraken2 = false
use_phamb = false
// ============================= Decontamination =============================
decontam = null
decontam_min_similarity = 0.95
// contamref_idx = "/project/genomics/jru/data2/db/viroprofiler/contamination_refs/hg19/ref"
contamref_idx = "${HOME}/viroprofiler/contamination_refs/hg19/ref"
// ============================= Contig library ==============================
assembler = "spades"
assemblies = "scaffolds" // ["contigs","scaffolds"]
contig_minlen = 3000
contig_cluster_min_similarity = 95 // 0-100
contig_cluster_min_coverage = 85 // 0-100
// ============================= Gene library ==============================
prot_cluster_min_similarity = 0.7 // Minimum similarity of protein AA seqs in the same cluster
prot_cluster_min_coverage = 0.9 // Minimum similarity of protein AA seqs in the same cluster
gene_cluster_min_similarity = 0.9 // Minimum similarity of gene DNA seqs in the same cluster
gene_cluster_min_coverage = 0.9 // Minimum similarity of gene DNA seqs in the same cluster
// ============================= Binning =====================================
binning = false // "phamb", "vrhyme" or false
binning_minlen_contig = 5000
binning_minlen_bin = 5000
dvf_qvalue = 0.1
// ============================= Viral detection =============================
// virsorter2_groups = "dsDNAphage,NCLDV,RNA,ssDNA,lavidaviridae"
virsorter2_groups = "dsDNAphage"
// ============================= Taxonomy ====================================
contig_minlen_vcontact2 = 10000
pc_inflation = 1.5
vc_inflation = 1.5
taxa_db_source = "NCBI"
// ============================= Replication cycle ===========================
replicyc = "bacphlip" // ["replidec","bacphlip"]
// kraken2 + bracken
kraken2_db = "viral"
kraken2_clean = true
save_output_fastqs = false
save_reads_assignment = false
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Other options
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '8.GB'
max_cpus = 1
max_time = '12.h'
}
// 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")
///}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
standard {
process.executor = 'local'
process.cpus = 1
process.memory = 1.GB
}
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_denglab {
includeConfig 'conf/test.config'
includeConfig 'custom.config'
}
// Custom profiles for the denglab
charliecloud_denglab {
charliecloud.runOptions = "-b /dss -b /gpfs"
}
slurm_denglab2 {
process.executor = 'slurm'
process.cpus = { check_max( 1 * task.attempt, 'cpus') }
process.memory = { check_max( 2.GB * task.attempt, 'memory') }
process.queue = 'serial_std'
process.clusterOptions = '--clusters=serial'
process.time = { check_max( 12.h * task.attempt, 'time') }
}
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// 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"
}
process {
withLabel: setup {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 8.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: ABRICATE {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 2.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: ABUNDANCE {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 1.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: BACPHLIP {
ext.args = "--multi_fasta"
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 2.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: CHECKV {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: CONTIGLIB {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: CONTIGLIB_CLUSTER {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DB_DRAM {
cpus ={ check_max( 2 * task.attempt, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: DB_KRAKEN2 {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 1.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DB_VIBRANT {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DB_VIRSORTER2 {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DB_VREFSEQ {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DECONTAM {
ext.args = 'maxindel=1 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 pigz=True untrim'
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: DRAMV {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 6.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: DVF {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 20.h * task.attempt, 'time') }
}
withName: EMAPPER {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: FASTQC {
ext.args = '--quiet'
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 2.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: FASTP {
ext.args = "--detect_adapter_for_pe -p -n 1 -l 30 -5 -W 4 -M 20 -r -c -g -x"
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 2.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: GENEPRED {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 2.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: MAPPING2CONTIGS {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: MICOMPLETEDB {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: MULTIQC {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 1.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: NRSEQS {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: PHAMB_RF {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: REPLIDEC {
cpus = { check_max( 2 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: SPADES {
ext.args = "--meta"
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: TAXONOMY_MERGE {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 1.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: TAXONOMY_MMSEQS {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 6.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: TAXONOMY_VCONTACT {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
time = { check_max( 30.h * task.attempt, 'time') }
}
withName: VAMB {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 6.GB * task.attempt, 'memory') }
time = { check_max( 20.h * task.attempt, 'time') }
}
withName: VIBRANT {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 20.h * task.attempt, 'time') }
}
withName: VIRALHOST_IPHOP {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 6.GB * task.attempt, 'memory') }
time = { check_max( 40.h * task.attempt, 'time') }
}
withName: VIRSORTER2 {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 40.h * task.attempt, 'time') }
}
withName: VOGDB {
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
withName: VRHYME {
ext.args = "--method longest"
cpus = { check_max( 1 * task.attempt, 'cpus') }
memory = { check_max( 4.GB * task.attempt, 'memory') }
time = { check_max( 12.h * task.attempt, 'time') }
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'ViroProfiler'
author = 'Jinlong Ru'
homePage = 'https://github.com/deng-lab/viroprofiler'
description = 'A containerized bioinformatics pipeline for viral metagenomic data analysis'
mainScript = 'main.nf'
nextflowVersion = '>=22.04.0'
version = '0.2.4'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}