/* * ------------------------------------------------- * nf-core/hic Nextflow config file * ------------------------------------------------- * Default config options for all environments. * Cluster-specific config options should be saved * in the conf folder and imported under a profile * name here. */ // Global default params, used in configs params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :latest container = 'nfcore/hic:latest' // Workflow flags // TODO nf-core: Specify your pipeline's command line flags reads = "data/*{1,2}.fastq.gz" singleEnd = false outdir = './results' // Boilerplate options name = false multiqc_config = "$baseDir/conf/multiqc_config.yaml" email = false plaintext_email = false help = false igenomes_base = "./iGenomes" tracedir = "${params.outdir}/pipeline_info" clusterOptions = false awsqueue = false awsregion = 'eu-west-1' igenomesIgnore = false custom_config_version = 'master' } // Load base.config by default for all pipelines includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config" profiles { awsbatch { includeConfig 'conf/awsbatch.config' } conda { process.conda = "$baseDir/environment.yml" } debug { process.beforeScript = 'echo $HOSTNAME' } docker { docker.enabled = true process.container = params.container } singularity { singularity.enabled = true process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"} } test { includeConfig 'conf/test.config' } } // Load igenomes.config if required if(!params.igenomesIgnore){ includeConfig 'conf/igenomes.config' } // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] timeline { enabled = true file = "${params.tracedir}/nf-core/hic_timeline.html" } report { enabled = true file = "${params.tracedir}/nf-core/hic_report.html" } trace { enabled = true file = "${params.tracedir}/nf-core/hic_trace.txt" } dag { enabled = true file = "${params.tracedir}/nf-core/hic_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 = '>=0.32.0' version = '1.0dev' } // 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 } } }