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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UPHL-BioNGS/Cecret Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
sample_sheet = params.input
reads = null
single_reads = null
fastas = null
multifastas = null
nanopore = null
sra_accessions = []
genome_accessions = []
primer_bed = null
amplicon_bed = null
primer_set = 'ncov_V5.3.2'
reference_genome = null
gff = null
outdir = 'cecret'
species = 'sarscov2'
//# specifying the core workflow
trimmer = 'ivar'
cleaner = 'seqyclean'
aligner = 'bwa'
msa = 'mafft'
//# to toggle off processes
artic = true
artic_filter = true
aci = false
bbnorm = false
bcftools_variants = true
fastqc = true
igv_reports = false
ivar_variants = false
samtools_qc = true
samtools_ampliconstats = true
samtools_plot_ampliconstats = true
markdup = false
filter = false
multiqc = true
//# for optional route of tree generation and counting snps between samples
relatedness = false
snpdists = true
iqtree2 = true
heatcluster = true
phytreeviz = true
//# parameters for processes with their default values
aci_options = ''
artic_options = '--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360'
artic_read_filtering_options = '--min-length 400 --max-length 700'
bbnorm_options = 'target=200 min=5'
bcftools_variants_options = ''
fastp_options = ''
fastqc_options = ''
filter_options = ''
heatcluster_options = '-t png'
igv_reports_options = '--flanking 1000'
iqtree2_options = '-ninit 2 -n 2 -me 0.05 -m GTR'
ivar_consensus_options = '-q 20 -t 0.6 -n N'
ivar_trim_options = ''
ivar_variants_options = '-q 20 -t 0.6'
minimap2_options = '-K 20M'
minimum_depth = 100
mpileup_depth = 8000
multiqc_options = ''
mafft_options = '--maxambiguous 0.5'
phytreeviz_options = ''
samtools_ampliconclip_options = ''
samtools_coverage_options = ''
samtools_flagstat_options = ''
samtools_depth_options = ''
samtools_stats_options = ''
samtools_ampliconstats_options = '--max-amplicon-length 3000 --max-amplicons 3000'
samtools_plot_ampliconstats_options = '-size 1200,900 -size2 1200,900 -size3 1200,900'
samtools_markdup_options = ''
samtools_fixmate_options = ''
seqyclean_contaminant_file = '/Adapters_plus_PhiX_174.fasta'
seqyclean_options = '-minlen 25 -qual'
snpdists_options = '-c'
//# for optional contamination determination
kraken2 = false
kraken2_db = null
kraken2_options = ''
//# for using an included version of nextclade dataset
download_nextclade_dataset = true
//# organism specific
freyja = true
freyja_aggregate = true
nextclade = true
pangolin = true
pango_aliasor = true
vadr = true
pangolin_options = ''
pango_aliasor_options = ''
vadr_mdir = '/opt/vadr/vadr-models'
vadr_reference = 'sarscov2'
vadr_options = '--split --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn'
vadr_trim_options = '--minlen 50 --maxlen 30000'
nextclade_options = ''
nextclade_dataset = 'sars-cov-2'
freyja_variants_options = ''
freyja_demix_options = ''
iqtree2_outgroup = 'MN908947'
freyja_aggregate_options = ''
freyja_plot_options = ''
freyja_plot_filetype = 'png'
// the following were stolen from other nf-core workflows and may have no functionality here
// Boilerplate options
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = 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/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationShowHiddenParams = false
validate_params = true
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
//########## Setting the Profile ##########
profiles {
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)'
}
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
}
artic_V3 {
params.primer_set = 'ncov_V3'
}
artic_V4 {
params.primer_set = 'ncov_V4'
}
artic_V4_1 {
params.primer_set = 'ncov_V4.1'
}
artic_V5_3_2 {
params.primer_set = 'ncov_V5.3.2'
}
sarscov2 {
includeConfig './conf/sarscov2.config'
}
mpx {
includeConfig './conf/mpx.config'
}
mpx_idt {
includeConfig './conf/mpx_idt.config'
}
mpx_primalseq {
includeConfig './conf/mpx_primalseq.config'
}
mpx_yale {
includeConfig './conf/mpx_yale.config'
}
wastewater {
includeConfig './conf/sarscov2_wastewater.config'
}
uphl {
includeConfig './conf/uphl.config'
}
test {
includeConfig './conf/test.config'
}
test1 {
includeConfig './conf/test1.config'
}
test2 {
includeConfig './conf/test2.config'
}
test3 {
includeConfig './conf/test3.config'
}
test_full {
includeConfig 'conf/test.config'
}
latest {
includeConfig 'conf/latest.config'
}
}
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 values ##########
manifest {
mainScript = 'main.nf'
nextflowVersion = '>=24.04.4'
name = 'UPHL-BioNGS/Cecret'
author = 'Erin Young'
homePage = 'https://github.com/UPHL-BioNGS/Cecret'
version = 'v3.25.25007'
defaultBranch = 'master'
recurseSubmodules = false
description = 'Reference-based consensus creation'
doi = ''
}
//######## nf-core assistance #####
validation {
help {
enabled = true
command = "nextflow run UPHL-BioNGS/Cecret -profile <docker/singularity/.../institute> --sample_sheet samplesheet.csv --outdir cecret"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
}
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'