80 lines
1.7 KiB
Plaintext
80 lines
1.7 KiB
Plaintext
//
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// Notes to End Users.
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//
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// The workflow should run without editing this configuration file,
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// however there may be instances in which you wish to edit this
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// file for compute performance or other reasons. Please see:
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//
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// https://nextflow.io/docs/latest/config.html#configuration
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//
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// for further help editing this file.
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params {
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help = false
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out_dir = "output"
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wfversion = "v0.0.1"
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}
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executor {
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$local {
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cpus = 4
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memory = "8 GB"
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}
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}
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profiles {
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// the "standard" profile is used implicitely by nextflow
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// if no other profile is given on the CLI
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standard {
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docker {
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enabled = true
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// this ensures container is run as host user and group, but
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// also adds host user to the within-container group
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runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
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}
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process {
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withLabel:pysam {
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container = "ontresearch/wf-template:${params.wfversion}"
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}
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shell = ['/bin/bash', '-euo', 'pipefail']
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}
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}
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// profile using conda environments rather than docker
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// containers
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conda {
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docker {
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enabled = false
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}
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process {
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withLabel:pysam {
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conda = "environment.yaml"
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}
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shell = ['/bin/bash', '-euo', 'pipefail']
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}
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conda {
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cacheDir = ""
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}
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}
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}
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timeline {
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enabled = true
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file = "${params.out_dir}/execution_timeline.html"
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}
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report {
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enabled = true
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file = "${params.out_dir}/execution_report.html"
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}
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trace {
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enabled = true
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file = "${params.out_dir}/execution_trace.txt"
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}
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dag {
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enabled = true
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file = "${params.out_dir}/pipeline_dag.svg"
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}
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