From 2ff08d92da17f7ae78da85380f959dc3e74aa3e6 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 22:20:23 +0000 Subject: [PATCH] Adjust = to be same everywhere --- nextflow.config | 208 ++++++++++++++++++++++++------------------------ 1 file changed, 104 insertions(+), 104 deletions(-) diff --git a/nextflow.config b/nextflow.config index b1b24dbc..759cf40d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,84 +10,84 @@ params { // Input options - input = null + input = null // Workflow flags - protocol = 'illumina' + protocol = 'illumina' // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' - igenomes_ignore = false - mirna_gtf = null - mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz" - hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" - mirgenedb = false - mirgenedb_mature = null - mirgenedb_hairpin = null - mirgenedb_gff = null - mirgenedb_species = null + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_ignore = false + mirna_gtf = null + mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz" + hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" + mirgenedb = false + mirgenedb_mature = null + mirgenedb_hairpin = null + mirgenedb_gff = null + mirgenedb_species = null // Trimming options - clip_r1 = null - three_prime_clip_r1 = null - three_prime_adapter = null - trim_fastq = true - fastp_min_length = 17 - fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa" - save_trimmed_fail = false - skip_qc = false - skip_fastqc = false - skip_multiqc = false - skip_mirdeep = false - skip_fastp = false - save_reference = false - fastp_max_length = 40 + clip_r1 = null + three_prime_clip_r1 = null + three_prime_adapter = null + trim_fastq = true + fastp_min_length = 17 + fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa" + save_trimmed_fail = false + skip_qc = false + skip_fastqc = false + skip_multiqc = false + skip_mirdeep = false + skip_fastp = false + save_reference = false + fastp_max_length = 40 // Contamination filtering - filter_contamination = false - rrna = null - trna = null - cdna = null - ncrna = null - pirna = null - other_contamination = null + filter_contamination = false + rrna = null + trna = null + cdna = null + ncrna = null + pirna = null + other_contamination = null // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' multiqc_methods_description = null // Boilerplate options - outdir = null - tracedir = "${params.outdir}/pipeline_info" - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - enable_conda = false + outdir = null + tracedir = "${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 + validate_params = true + show_hidden_params = false + schema_ignore_params = 'genomes' + enable_conda = false // Config options - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null - config_profile_contact = null - config_profile_url = null - config_profile_name = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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' + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' } @@ -112,64 +112,64 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + params.enable_conda = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } mamba { - params.enable_conda = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + params.enable_conda = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } docker { - docker.enabled = true - docker.userEmulation = true - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + docker.userEmulation = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } singularity { - singularity.enabled = true - singularity.autoMounts = true - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } podman { - podman.enabled = true - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false + podman.enabled = true + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false } shifter { - shifter.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false + shifter.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false } charliecloud { - charliecloud.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false + charliecloud.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false } gitpod { - executor.name = 'local' - executor.cpus = 16 - executor.memory = 60.GB + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB } test { includeConfig 'conf/test.config' } test_no_genome { includeConfig 'conf/test_no_genome.config' }