281 lines
9.8 KiB
Text
281 lines
9.8 KiB
Text
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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nf-core/wartanalysis Nextflow config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Default config options for all compute environments
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----------------------------------------------------------------------------------------
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*/
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// Global default params, used in configs
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params {
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// TODO nf-core: Specify your pipeline's command line flags
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// Input options
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input = null
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// References
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genome = null
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igenomes_base = 's3://ngi-igenomes/igenomes/'
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igenomes_ignore = false
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// MultiQC options
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multiqc_config = null
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multiqc_title = null
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multiqc_logo = null
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max_multiqc_email_size = '25.MB'
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multiqc_methods_description = null
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// Boilerplate options
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outdir = null
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publish_dir_mode = 'copy'
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email = null
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email_on_fail = null
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plaintext_email = false
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monochrome_logs = false
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hook_url = null
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help = false
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version = false
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pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
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// Config options
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config_profile_name = null
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config_profile_description = null
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custom_config_version = 'master'
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custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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config_profile_contact = null
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config_profile_url = null
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// Max resource options
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// Defaults only, expecting to be overwritten
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max_memory = '128.GB'
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max_cpus = 16
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max_time = '240.h'
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// Schema validation default options
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validationFailUnrecognisedParams = false
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validationLenientMode = false
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validationSchemaIgnoreParams = 'genomes,igenomes_base'
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validationShowHiddenParams = false
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validate_params = true
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}
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// Load base.config by default for all pipelines
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includeConfig 'conf/base.config'
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// Load nf-core custom profiles from different Institutions
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try {
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includeConfig "${params.custom_config_base}/nfcore_custom.config"
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} catch (Exception e) {
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System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
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}
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// Load nf-core/wartanalysis custom profiles from different institutions.
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try {
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includeConfig "${params.custom_config_base}/pipeline/wartanalysis.config"
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} catch (Exception e) {
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System.err.println("WARNING: Could not load nf-core/config/wartanalysis profiles: ${params.custom_config_base}/pipeline/wartanalysis.config")
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}
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profiles {
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debug {
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dumpHashes = true
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process.beforeScript = 'echo $HOSTNAME'
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cleanup = false
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nextflow.enable.configProcessNamesValidation = true
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}
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conda {
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conda.enabled = true
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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conda.channels = ['conda-forge', 'bioconda', 'defaults']
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apptainer.enabled = false
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}
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mamba {
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conda.enabled = true
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conda.useMamba = true
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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apptainer.enabled = false
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}
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docker {
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docker.enabled = true
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conda.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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apptainer.enabled = false
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docker.runOptions = '-u $(id -u):$(id -g)'
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}
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arm {
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docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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conda.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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apptainer.enabled = false
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}
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podman {
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podman.enabled = true
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conda.enabled = false
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docker.enabled = false
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singularity.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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apptainer.enabled = false
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}
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shifter {
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shifter.enabled = true
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conda.enabled = false
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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charliecloud.enabled = false
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apptainer.enabled = false
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}
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charliecloud {
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charliecloud.enabled = true
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conda.enabled = false
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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apptainer.enabled = false
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}
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apptainer {
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apptainer.enabled = true
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apptainer.autoMounts = true
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conda.enabled = false
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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}
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wave {
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apptainer.ociAutoPull = true
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singularity.ociAutoPull = true
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wave.enabled = true
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wave.freeze = true
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wave.strategy = 'conda,container'
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}
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gitpod {
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executor.name = 'local'
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executor.cpus = 4
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executor.memory = 8.GB
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}
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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}
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// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
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// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
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// Set to your registry if you have a mirror of containers
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apptainer.registry = 'quay.io'
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docker.registry = 'quay.io'
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podman.registry = 'quay.io'
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singularity.registry = 'quay.io'
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// Nextflow plugins
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plugins {
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id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
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}
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// Load igenomes.config if required
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if (!params.igenomes_ignore) {
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includeConfig 'conf/igenomes.config'
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} else {
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params.genomes = [:]
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}
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// Export these variables to prevent local Python/R libraries from conflicting with those in the container
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// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
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// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
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env {
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PYTHONNOUSERSITE = 1
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R_PROFILE_USER = "/.Rprofile"
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R_ENVIRON_USER = "/.Renviron"
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JULIA_DEPOT_PATH = "/usr/local/share/julia"
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}
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// Capture exit codes from upstream processes when piping
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process.shell = ['/bin/bash', '-euo', 'pipefail']
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// Disable process selector warnings by default. Use debug profile to enable warnings.
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nextflow.enable.configProcessNamesValidation = false
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def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
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timeline {
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enabled = true
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file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
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}
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report {
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enabled = true
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file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
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}
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trace {
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enabled = true
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file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
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}
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dag {
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enabled = true
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file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
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}
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manifest {
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name = 'nf-core/wartanalysis'
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author = """Me"""
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homePage = 'https://github.com/nf-core/wartanalysis'
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description = """For NAAB"""
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mainScript = 'main.nf'
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nextflowVersion = '!>=23.04.0'
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version = '1.0dev'
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doi = ''
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}
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// Load modules.config for DSL2 module specific options
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includeConfig 'conf/modules.config'
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// Function to ensure that resource requirements don't go beyond
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// a maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min( obj, params.max_cpus as int )
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
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