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nextflow.config
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nextflow.config
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// Nextflow config
manifest {
homePage = 'https://github.com/blue-moon22/GBS_QC_nf'
description = "A NextFlow pipeline of Group B Strep QC"
mainScript = 'main.nf'
nextflowVersion = '>=20.10.0'
}
params {
rel_abund_threshold = 70
run_reads_qc = false
pf_version = "1.1.1"
lanes = ""
species = "'Streptococcus agalactiae'"
headers = "./headers.json"
python_version = "3.11.4-jupyter-v01"
contig_no_threshold = 500
assembler = "spades"
qc_reports_directory = "./"
gc_content_lower_threshold = 32
gc_content_higher_threshold = 38
genome_len_lower_threshold = 1450000
genome_len_higher_threshold = 2800000
cov_depth_threshold = 20
cov_breadth_threshold = 70
het_snps_threshold = 20
version = ""
}
env {
PYTHONPATH = "$baseDir"
HTTP_PROXY = "http://wwwcache.sanger.ac.uk:3128"
HTTPS_PROXY = "http://wwwcache.sanger.ac.uk:3128"
LC_CTYPE="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
}
profiles {
// Standard default configuration for an LSF FARM environment
standard {
docker {
enabled = false
}
singularity {
enabled = true
autoMounts = true
cacheDir = "$PWD"
}
process.cpus = 1
process.memory = "2GB"
process.queue = "normal"
process.errorStrategy = {task.attempt <= 1 ? 'retry' : 'terminate'}
maxRetries = 2
process.maxRetries = 3
executor {
name = "lsf"
// Maximum number of jobs to spawn at once - adjust as necessary
queueSize = 100
jobName = { "gbs_qc - $task.name - $task.hash" }
pollInterval = "5 sec"
}
}
}