101 lines
2.3 KiB
Plaintext
101 lines
2.3 KiB
Plaintext
//
|
|
// 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
|
|
fastq = null
|
|
out_dir = "output"
|
|
samples = null
|
|
sanitize_fastq = false
|
|
wfversion = "v0.0.7"
|
|
aws_image_prefix = null
|
|
aws_queue = null
|
|
report_name = "report"
|
|
}
|
|
|
|
|
|
executor {
|
|
$local {
|
|
cpus = 4
|
|
memory = "8 GB"
|
|
}
|
|
}
|
|
|
|
profiles {
|
|
// the "standard" profile is used implicitely by nextflow
|
|
// if no other profile is given on the CLI
|
|
standard {
|
|
docker {
|
|
enabled = true
|
|
// this ensures container is run as host user and group, but
|
|
// also adds host user to the within-container group
|
|
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
|
|
}
|
|
process {
|
|
withLabel:pysam {
|
|
container = "ontresearch/wf-template:${params.wfversion}"
|
|
}
|
|
shell = ['/bin/bash', '-euo', 'pipefail']
|
|
}
|
|
}
|
|
|
|
// profile using conda environments rather than docker
|
|
// containers
|
|
conda {
|
|
docker {
|
|
enabled = false
|
|
}
|
|
process {
|
|
withLabel:pysam {
|
|
conda = "${projectDir}/environment.yaml"
|
|
}
|
|
shell = ['/bin/bash', '-euo', 'pipefail']
|
|
}
|
|
conda {
|
|
cacheDir = ""
|
|
useMamba = true
|
|
}
|
|
}
|
|
|
|
awsbatch {
|
|
process {
|
|
executor = 'awsbatch'
|
|
queue = "${params.aws_queue}"
|
|
memory = '8G'
|
|
withLabel:pysam {
|
|
container = "${params.aws_image_prefix}-wf-template:${params.wfversion}"
|
|
}
|
|
shell = ['/bin/bash', '-euo', 'pipefail']
|
|
}
|
|
}
|
|
aws.region = 'eu-west-1'
|
|
aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
|
|
}
|
|
|
|
|
|
timeline {
|
|
enabled = true
|
|
file = "${params.out_dir}/execution/timeline.html"
|
|
}
|
|
report {
|
|
enabled = true
|
|
file = "${params.out_dir}/execution/report.html"
|
|
}
|
|
trace {
|
|
enabled = true
|
|
file = "${params.out_dir}/execution/trace.txt"
|
|
}
|
|
dag {
|
|
enabled = true
|
|
file = "${params.out_dir}/execution/pipeline.svg"
|
|
}
|