/* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/hic Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- */ // Global default params, used in configs params { // Choice of the workflow ('hicpro' or 'hicstuff') workflow = 'hicpro' // Input options input = null // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false chromosome_size = null restriction_fragments = null save_reference = false // Mapping split_fastq = false fastq_chunks_size = 20000000 save_interaction_bam = false save_aligned_intermediates = false bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder' bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder' keep_dups = false keep_multi = false filter_pcr_picard = false min_mapq = 10 // Digestion Hi-C digestion = null ligation_site = null restriction_site = null digest { 'hindiii'{ restriction_site='A^AGCTT' ligation_site='AAGCTAGCTT' } 'mboi' { restriction_site='^GATC' ligation_site='GATCGATC' } 'dpnii' { restriction_site='^GATC' ligation_site='GATCGATC' } 'arima' { restriction_site='^GATC,G^ANTC' ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC' } } min_restriction_fragment_size = 0 max_restriction_fragment_size = 0 min_insert_size = 0 max_insert_size = 0 save_pairs_intermediates = false // Dnase Hi-C dnase = false min_cis_dist = 0 // Contact maps save_raw_maps = false bin_size = '1000000' res_zoomify = null hicpro_maps = false ice_max_iter = 100 ice_filter_low_count_perc = 0.02 ice_filter_high_count_perc = 0 ice_eps = 0.1 // Downstream Analysis res_dist_decay = '250000' tads_caller = 'insulation' res_tads = '40000' res_compartments = '250000' // Workflow skip_maps = false skip_balancing = false skip_mcool = false skip_dist_decay = false skip_compartments = false skip_tads = false skip_multiqc = false skip_plot_matrix = false // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null // Boilerplate options outdir = './results' tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null plaintext_email = false monochrome_logs = false hook_url = null help = false version = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,digest,bin_size,res_dist_decay,res_tads,res_compartments' // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_description = null config_profile_contact = null config_profile_url = null config_profile_name = null // Max resource options // Defaults only, expecting to be overwritten max_memory = '128.GB' max_cpus = 16 max_time = '240.h' // Hicstuff hicstuff_bwt2_align_opts = '--very-sensitive-local' hicstuff_min_size = 0 hicstuff_circular = 'false' hicstuff_output_contigs = 'info_contigs.txt' hicstuff_output_frags = 'fragments_list.txt' hicstuff_frags_plot = 'false' hicstuff_frags_plot_path = 'frags_hist.pdf' hicstuff_valid_pairs = 'valid.pairs' hicstuff_valid_idx = 'valid_idx.pairs' hicstuff_min_qual = 30 hicstuff_matrix = 'abs_fragments_contacts_weighted.txt' hicstuff_bin = 10000 hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs' hicstuff_plot_events = 'false' hicstuff_pie_plot = 'distrib' hicstuff_dist_plot = 'dist' hicstuff_centro_file = 'None' //give absolute path or 'None' hicstuff_base = 1.1 hicstuff_distance_out_file = 'distance_law.txt' hicstuff_rm_centro = 'None' //string number (ex: '30') or 'None' hicstuff_distance_plot = 'false' hicstuff_distance_out_plot = 'plot_distance_law.pdf' hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs' //Hicstuff optional modules filter_event = false distance_law = false filter_pcr = false } // Load base.config by default for all pipelines includeConfig 'conf/base.config' // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.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: ${params.custom_config_base}/nfcore_custom.config") } // Load nf-core/hic custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! // try { // includeConfig "${params.custom_config_base}/pipeline/hic.config" // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/hic profiles: ${params.custom_config_base}/pipeline/hic.config") // } profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false } conda { conda.enabled = true docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false } mamba { conda.enabled = true conda.useMamba = true docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false } docker { docker.enabled = true docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true singularity.autoMounts = true conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false } podman { podman.enabled = true podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false } shifter { shifter.enabled = true conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false apptainer.enabled = false } charliecloud { charliecloud.enabled = true conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false apptainer.enabled = false } apptainer { apptainer.enabled = true conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false } gitpod { executor.name = 'local' executor.cpus = 16 executor.memory = 60.GB } public_aws_ecr { includeConfig 'conf/public_aws_ecr.config' } 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' } else { params.genomes = [:] } // Export these variables to prevent local Python/R libraries from conflicting with those in the container // 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. // 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. env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" } // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] // Set default registry for Docker and Podman independent of -profile // Will not be used unless Docker / Podman are enabled // Set to your registry if you have a mirror of containers docker.registry = 'quay.io' podman.registry = 'quay.io' def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" } report { enabled = true file = "${params.tracedir}/execution_report_${trace_timestamp}.html" } trace { enabled = true file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" } dag { enabled = true file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" } 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 = '!>=22.10.1' version = '2.1.0' doi = '' } // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' // 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 } } }