fixed nextflow config for micromamba use

Author: saramonzon

nextflow.config

@@ -53,85 +53,88 @@ profiles {
   }
 
   conda {
+	conda.enabled = true
+	//conda.useMicromamba = true
+    	//conda.channels = 'conda-forge,bioconda,defaults'
   	process{
-  		// conda= "/opt/miniconda3/envs/bacterial_wgs_training/"
+  		// conda= "/opt/micromamba/envs/bacterial_wgs_training/"
   		withName:makeBWAindex {
-    		conda = "/opt/miniconda3/envs/bwa/"
+    		conda = "/opt/micromamba/envs/bwa/"
   		}
   		withName:fastqc {
-    		conda = "/opt/miniconda3/envs/fastqc/"
+    		conda = "/opt/micromamba/envs/fastqc/"
   		}
   		withName:trimming {
-    		conda = "/opt/miniconda3/envs/fastp/"
+    		conda = "/opt/micromamba/envs/fastp/"
   		}
   		withName:bwa {
-    		conda = "/opt/miniconda3/envs/bwa/"
+    		conda = "/opt/micromamba/envs/bwa/"
   		}
   		withName:samtools {
-    		conda = "/opt/miniconda3/envs/mapping/"
+    		conda = "/opt/micromamba/envs/mapping/"
   		}
   		withName:bwa_mapped {
-    		conda = "/opt/miniconda3/envs/mapping/"
+    		conda = "/opt/micromamba/envs/mapping/"
   		}
   		withName:picard {
-    		conda = "/opt/miniconda3/envs/mapping/"
+    		conda = "/opt/micromamba/envs/mapping/"
   		}
   		withName:unicycler {
-    		conda = "/opt/miniconda3/envs/unicycler/"
+    		conda = "/opt/micromamba/envs/unicycler/"
   		}
   		withName:quast {
-    		conda = "/opt/miniconda3/envs/quast/"
+    		conda = "/opt/micromamba/envs/quast/"
   		}
   		withName:prokka {
-    		conda = "/opt/miniconda3/envs/prokka/"
+    		conda = "/opt/micromamba/envs/prokka/"
   		}
   		withName:snippy {
-    		conda = "/opt/miniconda3/envs/samtools/"
+    		conda = "/opt/micromamba/envs/snippy/"
   		}
   		withName:snippy_core {
-    		conda = "/opt/miniconda3/envs/samtools/"
+    		conda = "/opt/micromamba/envs/snippy/"
   		}
   		withName:gubbins {
-    		conda = "/opt/miniconda3/envs/snippy/"
+    		conda = "/opt/micromamba/envs/snippy/"
   		}
   		withName:iqtree {
-    		conda = "/opt/miniconda3/envs/iqtree/"
+    		conda = "/opt/micromamba/envs/iqtree/"
   		}
   		withName:scheme_evaluation {
-    		conda = "/opt/miniconda3/envs/taranis/"
+    		conda = "/opt/micromamba/envs/taranis/"
   		}
   		withName:taranis {
-    		conda = "/opt/miniconda3/envs/taranis/"
+    		conda = "/opt/micromamba/envs/taranis/"
   		}
   		withName:plasmidid {
-    		conda = "/opt/miniconda3/envs/plasmidid/"
+    		conda = "/opt/micromamba/envs/plasmidid/"
   		}
   		withName:srst2_virulence {
-    		conda = "/opt/miniconda3/envs/srst2/"
+    		conda = "/opt/micromamba/envs/srst2/"
   		}
   		withName:srst2_mlst {
-    		conda = "/opt/miniconda3/envs/srst2/"
+    		conda = "/opt/micromamba/envs/srst2/"
   		}
   		withName:srst2_serogroup {
-    		conda = "/opt/miniconda3/envs/srst2/"
+    		conda = "/opt/micromamba/envs/srst2/"
   		}
   		withName:srst2_resistance {
-    		conda = "/opt/miniconda3/envs/srst2/"
+    		conda = "/opt/micromamba/envs/srst2/"
   		}
   		withName:multiqc_preprocessing {
-    		conda = "/opt/miniconda3/envs/multiqc/"
+    		conda = "/opt/micromamba/envs/multiqc/"
   		}
   		withName:multiqc_mapping {
-    		conda = "/opt/miniconda3/envs/multiqc/"
+    		conda = "/opt/micromamba/envs/multiqc/"
   		}
   		withName:multiqc_assembly {
-    		conda = "/opt/miniconda3/envs/multiqc/"
+    		conda = "/opt/micromamba/envs/multiqc/"
   		}
   		withName:multiqc_outbreakSNP {
-    		conda = "/opt/miniconda3/envs/multiqc/"
+    		conda = "/opt/micromamba/envs/multiqc/"
   		}
   		withName:multiqc_preprocessing {
-    		conda = "/opt/miniconda3/envs/multiqc/"
+    		conda = "/opt/micromamba/envs/multiqc/"
   		}
     }
   }