/* * ------------------------------------------------- * nf-core/hic Nextflow config file * ------------------------------------------------- * Default config options for all environments. */ // Global default params, used in configs params { // Workflow flags // TODO nf-core: Specify your pipeline's command line flags genome = false input = null input_paths = null single_end = false outdir = './results' publish_dir_mode = 'copy' // Boilerplate options multiqc_config = false email = false email_on_fail = false max_multiqc_email_size = 25.MB plaintext_email = false monochrome_logs = false help = false igenomes_base = 's3://ngi-igenomes/igenomes/' tracedir = "${params.outdir}/pipeline_info" igenomes_ignore = false custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" hostnames = false config_profile_description = false config_profile_contact = false config_profile_url = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,input_paths' // Defaults only, expecting to be overwritten max_memory = 128.GB max_cpus = 16 max_time = 240.h } // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev process.container = 'nfcore/hic:dev' // Load base.config by default for all pipelines includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions try { includeConfig "${params.custom_config_base}/nfcore_custom.config" } catch (Exception e) { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } profiles { conda { docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud = false process.conda = "$projectDir/environment.yml" } debug { process.beforeScript = 'echo $HOSTNAME' } docker { docker.enabled = true singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false // Avoid this error: // WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351 // once this is established and works well, nextflow might implement this behavior as new default. docker.runOptions = '-u \$(id -u):\$(id -g)' } singularity { docker.enabled = false singularity.enabled = true podman.enabled = false shifter.enabled = false charliecloud.enabled = false singularity.autoMounts = true } podman { singularity.enabled = false docker.enabled = false podman.enabled = true shifter.enabled = false charliecloud = false } shifter { singularity.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = true charliecloud.enabled = false } charliecloud { singularity.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = true } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } // Load igenomes.config if required if (!params.igenomes_ignore) { includeConfig 'conf/igenomes.config' } // Export these variables to prevent local Python/R libraries from conflicting with those in the container env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" } // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] timeline { enabled = true file = "${params.tracedir}/execution_timeline.html" } report { enabled = true file = "${params.tracedir}/execution_report.html" } trace { enabled = true file = "${params.tracedir}/execution_trace.txt" } dag { enabled = true file = "${params.tracedir}/pipeline_dag.svg" } manifest { name = 'nf-core/hic' author = 'Nicolas Servant' homePage = 'https://github.com/nf-core/hic' description = 'Analysis of Chromosome Conformation Capture data (Hi-C)' mainScript = 'main.nf' nextflowVersion = '>=20.04.0' version = '1.3.0dev' } // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { if (type == 'memory') { try { if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) return params.max_memory as nextflow.util.MemoryUnit else return obj } catch (all) { println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" return obj } } else if (type == 'time') { try { if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) return params.max_time as nextflow.util.Duration else return obj } catch (all) { println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" return obj } } else if (type == 'cpus') { try { return Math.min( obj, params.max_cpus as int ) } catch (all) { println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" return obj } } }