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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/bacpaq 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 // location for the input samplesheet file
classifier = "kraken2"
fasta = "test.fa"
schema_ignore_params = "fasta"
tracedir = "null"
//rasusa subsampling options
skip_subsampling = true
depth_cut_off = '50' // minimum coverage to subsample the reads is 50
// assembly_qc: genomesize is used by confindr for spec
subsampling_genomesize = 5000000 // change name - de-group from reads reference genome size. Valid metric suffixes include Base (b), Kilo (k), Mega (m), Giga (g), Tera (t)
//confindr options
skip_confindr = false
confindr_db = "/mnt/cidgoh-object-storage/database/confindr/confindr_db" //database for confindr. The default database are only for detecting contamination in Escherichia, Listeria, and Salmonella. If you want to run ConFindr on any other genera, you need to build the database following the tutorial at https://olc-bioinformatics.github.io/ConFindr/install/.
//QC options
skip_seqqc = false
skip_trimming = false
trim_tool = "fastp" // Select which trimming tool to use (fastp/trimmomatic/trimgalore)
adapter_fasta = "/mnt/cidgoh-object-storage/database/adaptors/test.fa" // location for adapator database (fasta file)
save_trimmed_fail = false // Check if reads failed in the trimming process need to be saved (True/False, default: False)
save_merged = true // Check if merged reads need to be saved (True/False, default: True)
// MultiQC options
max_multiqc_email_size = '25.MB'
multiqc_title = "BACPAQ"
multiqc_config = "null"
multiqc_logo = "null"
multiqc_methods_description= "null"
// Nanopore QC options
skip_nanocomp = false
skip_pycoqc = false
skip_porechop = false
// PycoQC options
// Path to nanopore summary file to be used by PycoQC
nanopore_summary_file = "/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/run_summary/sequencing_summary_FAT24492_18678559.txt"
// ID for nanopore summary file to be used by PycoQC
nanopore_summary_file_id = 'test'
// Assembly options (Dragonflye/Shovill)
// Estimated genome size, e.g. 3.2M (autodetect: blank)
assembly_genomesize = "''"
// Minimum contig length (auto: 0)
min_contig_len = 500
// Minimum contig coverage (auto: 0)
min_contig_coverage = 2
// Dragonflye options
// Minimum input read length (disable: 0)
min_input_read_len = 1000
// Minimum average sequence quality (off: 0)
min_input_quality = 0
// Number of polishing rounds to conduct with Racon
racon_rounds = 1
// Number of polishing rounds to conduct with Medaka (requires a model to be specified)
medaka_rounds = 1
// Path to model to be used for Medaka
medaka_model = "r941_min_fast_g507"
// Taxonomy module options
// Dehosting options
skip_dehosting = false
skip_combinekreports = false
skip_kreport2krona = false
skip_bracken = false
skip_kraken2 = false
skip_combinebrackenoutputs = false
// kraken2 options
// Path to Kraken2 database used for querying reads during taxonomic classification
kraken2_db = "/mnt/cidgoh-object-storage/database/minikraken2/minikraken2_v2_8GB_201904_UPDATE"
// Boolean for whether to output classified reads as a fastq file
classified_reads = true
// Boolean for whether to output unclassified reads as a fastq file
unclassified_reads = true
// centrifuge options
centrifuge_db = "/mnt/cidgoh-object-storage/database/centrifuge"
save_unaligned = true
// Boolean for whether to save aligned reads to a fastq file
save_aligned = true
// Boolean for whether to save the output as a SAM file
sam_format = true
// Aligner used for dehosting ('minimap2' or 'bwa')
dehosting_aligner = 'minimap2'
// Path to (human) reference genome used for dehosting
host_genome = "/mnt/cidgoh-object-storage/database/reference_genomes/human/GRCh38.p14/GCF_000001405.40/GCF_000001405.40_GRCh38.p14_genomic.fna"
// ID/name for reference genome
host_genome_id = 'GRCh38'
// bwa options
// Whether to sort ('sort') or view ('view') the BAM file obtained from BWA
bwa_sort_bam = 'sort'
// minimap2 options
// Boolean on whether to output the alignment as a BAM file or a PAF file
bam_format = true
// Boolean on whether to get Minimap2 to generate CIGAR strings at the cg tag of the PAF file
cigar_paf_format = false
// Boolean on whether to get Minimap2 to move long CIGAR strings to the cg tag in the BAM file
cigar_bam = false
// samtools options
// Boolean for whether to get Samtools fastq to generate an interleaved fastq or to write to separate files
interleaved = false
// 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
version = false
validate_params = false
show_hidden_params = false
schema_ignore_params = 'genomes'
// assembly QC options
skip_checkm = false
skip_quast = false
skip_busco = false
// Shovill options
sr_assembler = 'spades' // WGS_ASSEMBLY: choice of genome assembler for short read data [skesa,spades,megahit,velvet]
// CheckM options
checkm_db = 'null' // ASSEMBLY_QC: path to local CheckM lineages directory
// QUAST options
reference_genome_fasta = "null" // ASSEMBLY_QC: path to reference genome file
reference_genome_gff = "null" // ASSEMBLY_QC: path to reference genome annotation file (.GFF)
combine_quast = false // ASSEMBLY_QC: whether to aggregate individual QUAST results file
// BUSCO options
busco_lineage = "bacteria" // ASSEMBLY_QC: the BUSCO lineage to use, or "auto" to automatically select lineage
busco_lineages_path = "/mnt/cidgoh-object-storage/database/busco" // ASSEMBLY_QC: path to local BUSCO lineages directory
busco_config = false // ASSEMBLY_QC: path to BUSCO config file
// PEPPAN options
reference_gff = null
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// pipeline options
skip_QC = false
skip_taxonomy_qc = false
skip_assembly = false
skip_assembly_qc = false
skip_rmlst = false
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
/* Annotation options */
skip_annotation = false
skip_gene_annotation = false
skip_abricate_summary = false
amrfinderplus_db = null
skip_resfinder = false
skip_virsorter2 = false
skip_crispr_analysis = false
// AMR options
amr_finderplus_db = null
skip_amr_annotation = false
skip_rgi = false
skip_abricate = false
abricate_db = "card" // AMR: database to use for abricate
skip_abritamr = false
skip_amrfinderplus = false
resfinder_db = "/scratch/group_share/tmp/database/resfinder_db"
pointfinder_db = "/scratch/group_share/tmp/database/pointfinder_db"
disinfinder_db = "/scratch/group_share/tmp/database/disinfinder_db"
resfinder_species = "ecoli"
// gene annotation options
skip_gene_annotation = false
skip_prokka = false
skip_bakta = false
bakta_db = "/mnt/cidgoh-object-storage/database/bakta/db/"
prodigal_training_file = null
annotation_protein_file = null
// Phage options
skip_phage_annotation = false
virsorter_db = null
virsorter_virus_grp = 'dsDNAphage,ssDNA'
virsorter_min_len = 5000
virsorter_min_score = 0.4
// Pangenome options
skip_pangenome_analysis = false
pangenome_input = "bakta"
skip_roary = false
skip_pirate = false
skip_panaroo = false
clean_mode = "moderate"
skip_peppan = false
// Plasmid subworkflow options
skip_plasmid_analysis = false
skip_plasmidfinder = false
skip_mobsuite = false
// CRISPR subworkflow
skip_cctyper = false
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/bacpaq custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/bacpaq.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/bacpaq profiles: ${params.custom_config_base}/pipeline/bacpaq.config")
// }
//plugins {
// id 'nf-validation@0.2.1'
//}
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
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
}
eagle { includeConfig 'conf/eagle.config' }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
eagle_2 { includeConfig 'conf/eagle_2.config' }
}
// 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 = 'cidgoh/bacpaq'
author = """Zohaib Anwar, Jimmy Liu, Jun Duan, Aishwarya Sridhar, David Tong, Mathew Nguyen, Miguel Prieto, Michael Trimble, Soyean Kim and William Hsiao"""
homePage = 'https://github.com/cidgoh/bacpaq'
description = """Quality control workflow for short-reads (Illumina) and long-reads (Oxford Nanopore) sequencing data including WGS, Amplicon and Metagenomics"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.01.0'
version = '1.0dev'
doi = ''
}
// 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
}
}
}