From f1661e74f4346960c0e909694ce57b1c46786747 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 18 Oct 2023 10:42:22 +0200 Subject: [PATCH] new nextflow config --- nextflow.config | 72 +++++++++++++++++- nextflow_2.config | 190 ---------------------------------------------- 2 files changed, 69 insertions(+), 193 deletions(-) delete mode 100644 nextflow_2.config diff --git a/nextflow.config b/nextflow.config index c4c9001..1b5d785 100644 --- a/nextflow.config +++ b/nextflow.config @@ -54,9 +54,57 @@ profiles { conda { process{ - conda= "/opt/miniconda3/envs/bacterial_wgs_training/" - withName:srst2_resistance { - conda = "/opt/miniconda3/envs/srst2/" + // conda= "/opt/miniconda3/envs/bacterial_wgs_training/" + withName:makeBWAindex { + conda = "/opt/miniconda3/envs/bwa/" + } + withName:fastqc { + conda = "/opt/miniconda3/envs/fastqc/" + } + withName:trimming { + conda = "/opt/miniconda3/envs/fastp/" + } + withName:bwa { + conda = "/opt/miniconda3/envs/bwa/" + } + withName:samtools { + conda = "/opt/miniconda3/envs/mapping/" + } + withName:bwa_mapped { + conda = "/opt/miniconda3/envs/mapping/" + } + withName:picard { + conda = "/opt/miniconda3/envs/mapping/" + } + withName:unicycler { + conda = "/opt/miniconda3/envs/unicycler/" + } + withName:quast { + conda = "/opt/miniconda3/envs/quast/" + } + withName:prokka { + conda = "/opt/miniconda3/envs/prokka/" + } + withName:snippy { + conda = "/opt/miniconda3/envs/samtools/" + } + withName:snippy_core { + conda = "/opt/miniconda3/envs/samtools/" + } + withName:gubbins { + conda = "/opt/miniconda3/envs/snippy/" + } + withName:iqtree { + conda = "/opt/miniconda3/envs/iqtree/" + } + withName:scheme_evaluation { + conda = "/opt/miniconda3/envs/taranis/" + } + withName:taranis { + conda = "/opt/miniconda3/envs/taranis/" + } + withName:plasmidid { + conda = "/opt/miniconda3/envs/plasmidid/" } withName:srst2_virulence { conda = "/opt/miniconda3/envs/srst2/" @@ -67,6 +115,24 @@ profiles { withName:srst2_serogroup { conda = "/opt/miniconda3/envs/srst2/" } + withName:srst2_resistance { + conda = "/opt/miniconda3/envs/srst2/" + } + withName:multiqc_preprocessing { + conda = "/opt/miniconda3/envs/multiqc/" + } + withName:multiqc_mapping { + conda = "/opt/miniconda3/envs/multiqc/" + } + withName:multiqc_assembly { + conda = "/opt/miniconda3/envs/multiqc/" + } + withName:multiqc_outbreakSNP { + conda = "/opt/miniconda3/envs/multiqc/" + } + withName:multiqc_preprocessing { + conda = "/opt/miniconda3/envs/multiqc/" + } } } diff --git a/nextflow_2.config b/nextflow_2.config deleted file mode 100644 index 1b5d785..0000000 --- a/nextflow_2.config +++ /dev/null @@ -1,190 +0,0 @@ -/* - * ------------------------------------------------- - * 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. - */ - -manifest { - homePage = 'https://github.com/BU-ISCIII/bacterial_wgs_training' - description = 'This is a project for wgs analysis trainning using nextflow and containers.' - mainScript = 'main.nf' -} - -// Global default params, used in configs -params { - ver = '1.0' //Pipeline version - nf_required_version = '0.27.6' //Minimum version of Nextflow required - - reads="$baseDir/data/samples/*.fastq.gz" - outdir='results' - step = "preprocessing" - output_docs = "${baseDir}/docs/output.md" - multiqc_config = "${baseDir}/conf/multiqc_config.yaml" - // Mapping-duplicates defaults - keepduplicates = false - notrim = false - outbreaker_config = false - gtf = false - bwa_index = false - fasta = false - cut_mean_quality = 20 - qualified_quality_phred = 20 - unqualified_percent_limit = 10 - min_trim_length = 50 - scheme = false -} - -profiles { - - standard { - includeConfig 'conf/base.config' - } - - docker { - includeConfig 'conf/docker.config' - } - - singularity { - includeConfig 'conf/singularity.config' - } - - conda { - process{ - // conda= "/opt/miniconda3/envs/bacterial_wgs_training/" - withName:makeBWAindex { - conda = "/opt/miniconda3/envs/bwa/" - } - withName:fastqc { - conda = "/opt/miniconda3/envs/fastqc/" - } - withName:trimming { - conda = "/opt/miniconda3/envs/fastp/" - } - withName:bwa { - conda = "/opt/miniconda3/envs/bwa/" - } - withName:samtools { - conda = "/opt/miniconda3/envs/mapping/" - } - withName:bwa_mapped { - conda = "/opt/miniconda3/envs/mapping/" - } - withName:picard { - conda = "/opt/miniconda3/envs/mapping/" - } - withName:unicycler { - conda = "/opt/miniconda3/envs/unicycler/" - } - withName:quast { - conda = "/opt/miniconda3/envs/quast/" - } - withName:prokka { - conda = "/opt/miniconda3/envs/prokka/" - } - withName:snippy { - conda = "/opt/miniconda3/envs/samtools/" - } - withName:snippy_core { - conda = "/opt/miniconda3/envs/samtools/" - } - withName:gubbins { - conda = "/opt/miniconda3/envs/snippy/" - } - withName:iqtree { - conda = "/opt/miniconda3/envs/iqtree/" - } - withName:scheme_evaluation { - conda = "/opt/miniconda3/envs/taranis/" - } - withName:taranis { - conda = "/opt/miniconda3/envs/taranis/" - } - withName:plasmidid { - conda = "/opt/miniconda3/envs/plasmidid/" - } - withName:srst2_virulence { - conda = "/opt/miniconda3/envs/srst2/" - } - withName:srst2_mlst { - conda = "/opt/miniconda3/envs/srst2/" - } - withName:srst2_serogroup { - conda = "/opt/miniconda3/envs/srst2/" - } - withName:srst2_resistance { - conda = "/opt/miniconda3/envs/srst2/" - } - withName:multiqc_preprocessing { - conda = "/opt/miniconda3/envs/multiqc/" - } - withName:multiqc_mapping { - conda = "/opt/miniconda3/envs/multiqc/" - } - withName:multiqc_assembly { - conda = "/opt/miniconda3/envs/multiqc/" - } - withName:multiqc_outbreakSNP { - conda = "/opt/miniconda3/envs/multiqc/" - } - withName:multiqc_preprocessing { - conda = "/opt/miniconda3/envs/multiqc/" - } - } - } - - testing { - // TODO - } - - aws { - // TO DO - } - - none { - // Don't load any config (for use with custom home configs) - } - -} - -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] - -// By default output execution reports -timeline { - enabled = true - file = "${params.outdir}/timeline.html" -} -report { - enabled = true - file = "${params.outdir}/report.html" -} -trace { - enabled = true - file = "${params.outdir}/trace.txt" -} -dag { - enabled = true - file = "${params.outdir}/DAG.svg" -} - -// Function to ensure that resource requirements don't go beyond -// a maximum limit -//def check_max(obj, type) { -// if(type == 'memory'){ -// if(obj.compareTo(params.max_memory) == 1) -// return params.max_memory -// else -// return obj -// } else if(type == 'time'){ -// if(obj.compareTo(params.max_time) == 1) -// return params.max_time -// else -// return obj -// } else if(type == 'cpus'){ -// return Math.min( obj, params.max_cpus ) -// } -//}