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377 lines
13 KiB
Plaintext
377 lines
13 KiB
Plaintext
/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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nf-core/taxprofiler 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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// 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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tracedir = "${params.outdir}/pipeline_info"
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publish_dir_mode = 'copy'
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email = null
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email_on_fail = null
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plaintext_email = false
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monochrome_logs = false
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hook_url = null
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help = false
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version = false
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validate_params = true
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show_hidden_params = false
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schema_ignore_params = 'genomes,fasta'
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// Config options
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custom_config_version = 'master'
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custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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config_profile_description = null
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config_profile_contact = null
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config_profile_url = null
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config_profile_name = 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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// Databases
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databases = null
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// FASTQ preprocessing
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preprocessing_qc_tool = 'fastqc'
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perform_shortread_qc = false
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shortread_qc_tool = 'fastp'
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shortread_qc_skipadaptertrim = false
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shortread_qc_mergepairs = false
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shortread_qc_includeunmerged = false
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shortread_qc_adapter1 = null
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shortread_qc_adapter2 = null
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shortread_qc_adapterlist = null
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shortread_qc_minlength = 15
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perform_longread_qc = false
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longread_qc_skipadaptertrim = false
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longread_qc_skipqualityfilter = false
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longread_qc_qualityfilter_minlength = 1000
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longread_qc_qualityfilter_keeppercent = 90
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longread_qc_qualityfilter_targetbases = 500000000
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save_preprocessed_reads = false
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// Complexity filtering
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perform_shortread_complexityfilter = false
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shortread_complexityfilter_tool = 'bbduk'
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shortread_complexityfilter_entropy = 0.3
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shortread_complexityfilter_bbduk_windowsize = 50
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shortread_complexityfilter_bbduk_mask = false
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shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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shortread_complexityfilter_fastp_threshold = 30
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save_complexityfiltered_reads = false
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// run merging
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perform_runmerging = false
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save_runmerged_reads = false
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// Host Removal
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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hostremoval_reference = null
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shortread_hostremoval_index = null
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longread_hostremoval_index = null
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save_hostremoval_index = false
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save_hostremoval_bam = false
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save_hostremoval_unmapped = false
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// Publishing final reads going into profiling
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save_analysis_ready_fastqs = false
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// MALT
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run_malt = false
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malt_mode = 'BlastN'
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malt_generate_megansummary = false
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malt_save_reads = false // added via map + database args extension in profiling.nf
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// kraken2
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run_kraken2 = false
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kraken2_save_reads = false // added directly to module in profiling.nf
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kraken2_save_readclassification = false // added directly to module in profiling.nf
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kraken2_save_minimizers = false
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//krakenuniq
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run_krakenuniq = false
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krakenuniq_ram_chunk_size = '16G'
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krakenuniq_save_reads = false // added directly to module in profiling.nf
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krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
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krakenuniq_batch_size = 20
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// Bracken
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run_bracken = false
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// centrifuge
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run_centrifuge = false
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centrifuge_save_reads = false // added directly to module in profiling.nf
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// metaphlan3
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run_metaphlan3 = false
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// kaiju
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run_kaiju = false
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kaiju_taxon_rank = 'species'
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// diamond
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run_diamond = false
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diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
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diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
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// mOTUs
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run_motus = false
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motus_use_relative_abundance = false
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motus_remove_ncbi_ids = false
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motus_save_mgc_read_counts = false
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// krona
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run_krona = false
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krona_taxonomy_directory = null
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// profile standardisation
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run_profile_standardisation = false
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standardisation_taxpasta_format = 'tsv'
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taxpasta_taxonomy_dir = null
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taxpasta_add_name = false
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taxpasta_add_rank = false
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taxpasta_add_lineage = false
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taxpasta_add_idlineage = false
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standardisation_motus_generatebiom = false
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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: ${params.custom_config_base}/nfcore_custom.config")
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}
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// Load nf-core/taxprofiler custom profiles from different institutions.
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// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
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try {
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includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
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} catch (Exception e) {
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System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.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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}
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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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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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docker.registry = 'quay.io'
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docker.userEmulation = 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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}
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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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podman.registry = 'quay.io'
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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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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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gitpod {
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executor.name = 'local'
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executor.cpus = 16
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executor.memory = 60.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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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
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test_nothing { includeConfig 'conf/test_nothing.config' }
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test_motus { includeConfig 'conf/test_motus.config' }
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test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
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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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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 = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
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}
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report {
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enabled = true
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file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
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}
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trace {
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enabled = true
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file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
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}
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dag {
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enabled = true
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file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
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}
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manifest {
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name = 'nf-core/taxprofiler'
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author = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team"""
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homePage = 'https://github.com/nf-core/taxprofiler'
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description = """Taxonomic classification and profiling of shotgun and long-read metagenomic data"""
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mainScript = 'main.nf'
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nextflowVersion = '!>=22.10.1'
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version = '1.1.0dev'
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doi = '10.5281/zenodo.7728364'
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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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