/
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
fastq = null
bam = null
out_dir = "output"
sample = null
assembly = true
medaka_options = null
min_coverage = 20
aws_image_prefix = null
aws_queue = null
disable_ping = false
reference = "MT903344.1"
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,wf'
wf {
example_cmd = [
"--fastq 'wf-mpx-demo/fastq/barcode01'",
]
agent = null
container_sha = "sha22fc487196cad3768c9287fec8bf8524431d01a4"
common_sha = "sha91452ece4f647f62b32dac3a614635a6f0d7f8b5"
medaka_sha = "sha61a9438d745a78030738352e084445a2db3daa2a"
}
}
manifest {
name = 'epi2me-labs/wf-mpx'
author = 'Oxford Nanopore Technologies'
homePage = 'https://github.com/epi2me-labs/wf-mpx'
description = 'Mpox metagenomics assembly.'
mainScript = 'main.nf'
nextflowVersion = '>=23.04.2'
version = 'v1.0.0'
}
epi2melabs {
tags = 'metagenomics,assembly,viruses,public health'
icon = 'faVirus'
}
env {
PYTHONNOUSERSITE = 1
}
// used by default for "standard" (docker) and singularity profiles,
// other profiles may override.
process {
withLabel:wfmpx {
container = "ontresearch/wf-mpx:${params.wf.container_sha}"
}
withLabel:wf_common {
container = "ontresearch/wf-common:${params.wf.common_sha}"
}
withLabel:medaka {
container = "ontresearch/medaka:${params.wf.medaka_sha}"
}
shell = ['/bin/bash', '-euo', 'pipefail']
}
profiles {
// the "standard" profile is used implicitely by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures container is run as host user and group, but
// also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
}
// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
}
// keep stub conda profile to prevent unknown profile warning so users get a better error
conda {
conda.enabled = true
}
// Using AWS batch.
// May need to set aws.region and aws.batch.cliPath
awsbatch {
process {
executor = 'awsbatch'
queue = "${params.aws_queue}"
withLabel:wfmpx {
container = "${params.aws_image_prefix}-wf-mpx:${params.wf.container_sha}"
}
withLabel:wf_common {
container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}-root"
}
withLabel:medaka {
container = "${params.aws_image_prefix}-medaka:${params.wf.medaka_sha}-root"
}
shell = ['/bin/bash', '-euo', 'pipefail']
}
}
// local profile for simplified development testing
local {
process.executor = 'local'
}
}
timeline {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/timeline.html"
}
report {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/report.html"
}
trace {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/trace.txt"
}