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nextflow.config
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nextflow.config
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//
// Notes to End Users.
//
// The workflow should run without editing this configuration file,
// however there may be instances in which you wish to edit this
// file for compute performance or other reasons. Please see:
//
// https://nextflow.io/docs/latest/config.html#configuration
//
// for further help editing this file.
params {
help = false
version = false
analyse_unclassified = false
fastq = null
out_dir = "output"
sample = null
sample_sheet = null
reference = null
blastdb = null
min_coverage = 20
downsample = null
min_qscore = 9
align_threads = 4
wfversion = "v0.0.5"
aws_image_prefix = null
aws_queue = null
disable_ping = false
process_label = 'wfflu'
monochrome_logs = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion,wf'
wf {
example_cmd = [
"--fastq test_data/fastq"
]
flu_sha = "sha416819a0f4e681946651102f387d21e5a335ba98"
typing_sha = "shacd6e6b77d14424d746c3d7332dfa13e3bda9034f"
agent = null
}
}
manifest {
name = 'epi2me-labs/wf-flu'
author = 'Oxford Nanopore Technologies'
homePage = 'https://github.com/epi2me-labs/wf-flu'
description = 'Influenza A&B typing and analysis from Nanopore data.'
mainScript = 'main.nf'
nextflowVersion = '>=20.10.0'
version = 'v0.0.5'
}
epi2melabs {
tags = 'amplicon,viruses,public health'
icon = 'faViruses'
}
env {
PYTHONNOUSERSITE = 1
}
executor {
$local {
cpus = 4
memory = "8 GB"
}
}
profiles {
// the "standard" profile is used implicitely by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures container is run as host user and group, but
// also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
process {
withLabel:wfflu {
container = "ontresearch/wf-flu:${params.wf.flu_sha}"
}
withLabel:wfflutyping {
container = "ontresearch/abricate:${params.wf.typing_sha}"
}
}
}
// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
process {
withLabel:wfflu {
container = "ontresearch/wf-flu:${params.wf.flu_sha}"
}
withLabel:wfflutyping {
container = "ontresearch/abricate:${params.wf.typing_sha}"
}
}
}
// keep stub conda profile to prevent unknown profile warning so users get a better error
conda {
conda.enabled = true // required for 22.08
}
// Using AWS batch.
// May need to set aws.region and aws.batch.cliPath
awsbatch {
process {
executor = 'awsbatch'
queue = "${params.aws_queue}"
memory = '8G'
withLabel:wfflu {
container = "${params.aws_image_prefix}-wf-flu:${params.wf.flu_sha}-root"
}
withLabel:wfflutyping {
container = "${params.aws_image_prefix}-abricate:${params.wf.typing_sha}-root"
}
shell = ['/bin/bash', '-euo', 'pipefail']
}
}
// local profile for simplified development testing
local {
process.executor = 'local'
}
}
timeline {
enabled = true
file = "${params.out_dir}/execution/timeline.html"
}
report {
enabled = true
file = "${params.out_dir}/execution/report.html"
}
trace {
enabled = true
file = "${params.out_dir}/execution/trace.txt"
}