nextflow config with indv envs

nextflow_2.config

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+/*
+ * -------------------------------------------------
+ *  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/snippy/"
+  		}
+  		withName:snippy_core {
+    		conda = "/opt/miniconda3/envs/snippy/"
+  		}
+  		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 )
+//  }
+//}